Starting phenix.real_space_refine on Wed Nov 19 07:00:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c6l_7348/11_2025/6c6l_7348.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 14483 2.51 5 N 3547 2.21 5 O 3944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22110 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "C" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1488 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 395 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 550 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2793 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1143 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1143 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 6054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6054 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 724} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 5.30, per 1000 atoms: 0.24 Number of scatterers: 22110 At special positions: 0 Unit cell: (130.38, 116.85, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3944 8.00 N 3547 7.00 C 14483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 989.8 milliseconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5258 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 4 sheets defined 75.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'D' and resid 14 through 49 removed outlier: 4.148A pdb=" N PHE D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 60 through 81 removed outlier: 3.522A pdb=" N ILE D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 124 removed outlier: 3.687A pdb=" N MET D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 4.272A pdb=" N MET D 128 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.530A pdb=" N ILE D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 39 removed outlier: 3.546A pdb=" N VAL C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.557A pdb=" N PHE C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 4.013A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.557A pdb=" N LYS C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 123 removed outlier: 3.848A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 173 removed outlier: 3.637A pdb=" N PHE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 192 through 208 removed outlier: 3.514A pdb=" N GLY C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 245 removed outlier: 3.834A pdb=" N VAL N 229 " --> pdb=" O MET N 225 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER N 230 " --> pdb=" O CYS N 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER N 242 " --> pdb=" O ILE N 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP N 243 " --> pdb=" O VAL N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.580A pdb=" N ALA N 253 " --> pdb=" O THR N 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 24 removed outlier: 4.183A pdb=" N VAL M 8 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 removed outlier: 3.517A pdb=" N SER M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL M 37 " --> pdb=" O TRP M 33 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU M 41 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.915A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 3.632A pdb=" N ASN E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 76 removed outlier: 3.632A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 122 removed outlier: 3.681A pdb=" N PHE E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 89 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 153 removed outlier: 3.523A pdb=" N ILE E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 136 " --> pdb=" O ILE E 132 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 removed outlier: 4.234A pdb=" N ASN B 7 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 8 " --> pdb=" O TYR B 5 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 9 " --> pdb=" O PHE B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 9' Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.570A pdb=" N ARG B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.756A pdb=" N TYR B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.718A pdb=" N LEU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 116 removed outlier: 3.529A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASP B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.560A pdb=" N ILE B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 4.168A pdb=" N GLU B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 199 removed outlier: 3.598A pdb=" N ASN B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 231 removed outlier: 4.397A pdb=" N GLU B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.862A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.185A pdb=" N GLY B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.685A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 283 through 300 removed outlier: 4.191A pdb=" N HIS B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 332 removed outlier: 3.676A pdb=" N LYS B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.552A pdb=" N ILE B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 43 removed outlier: 4.204A pdb=" N PHE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.688A pdb=" N GLY F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 122 removed outlier: 3.961A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 153 removed outlier: 4.421A pdb=" N GLY F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 149 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 43 removed outlier: 3.786A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 16 " --> pdb=" O PHE G 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 4.102A pdb=" N PHE G 51 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 76 removed outlier: 3.752A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 70 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 122 removed outlier: 3.780A pdb=" N ILE G 89 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU G 91 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 153 removed outlier: 4.392A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 133 " --> pdb=" O MET G 129 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 43 removed outlier: 3.769A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.732A pdb=" N LEU H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 76 removed outlier: 3.795A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 122 removed outlier: 3.509A pdb=" N PHE H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 114 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 155 removed outlier: 4.328A pdb=" N GLY H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA H 136 " --> pdb=" O ILE H 132 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA H 147 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG H 153 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 3.778A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 45 No H-bonds generated for 'chain 'I' and resid 44 through 45' Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.876A pdb=" N LEU I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.811A pdb=" N MET I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 122 removed outlier: 3.574A pdb=" N ILE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER I 96 " --> pdb=" O GLY I 92 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE I 110 " --> pdb=" O PHE I 106 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN I 121 " --> pdb=" O ARG I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 153 removed outlier: 4.344A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I 131 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 132 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 149 " --> pdb=" O ILE I 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 43 removed outlier: 4.185A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 54 through 76 removed outlier: 3.563A pdb=" N ILE J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR J 76 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 122 removed outlier: 3.647A pdb=" N ILE J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 96 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER J 120 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 155 removed outlier: 4.470A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU J 149 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 154 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR J 155 " --> pdb=" O ASN J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 3.673A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 removed outlier: 3.844A pdb=" N LEU K 49 " --> pdb=" O ARG K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.811A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR K 76 " --> pdb=" O VAL K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 122 removed outlier: 3.538A pdb=" N VAL K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 155 removed outlier: 3.985A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 133 " --> pdb=" O MET K 129 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR K 155 " --> pdb=" O ASN K 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 43 removed outlier: 4.369A pdb=" N PHE L 12 " --> pdb=" O TYR L 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 77 removed outlier: 3.583A pdb=" N ILE L 62 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 122 removed outlier: 3.803A pdb=" N ILE L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN L 90 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER L 96 " --> pdb=" O GLY L 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 134 removed outlier: 4.135A pdb=" N GLY L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 130 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 152 removed outlier: 3.553A pdb=" N VAL L 138 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 147 " --> pdb=" O GLY L 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.609A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.559A pdb=" N ILE A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.546A pdb=" N TYR A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 145 removed outlier: 4.390A pdb=" N TYR A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.619A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.821A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 303 removed outlier: 3.683A pdb=" N ASN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 325 removed outlier: 4.196A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.982A pdb=" N ALA A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 407 through 423 removed outlier: 4.589A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.991A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 454 through 461 removed outlier: 3.776A pdb=" N ALA A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 removed outlier: 3.950A pdb=" N MET A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.724A pdb=" N TRP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 554 removed outlier: 3.968A pdb=" N LEU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.148A pdb=" N ASN A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 596 removed outlier: 3.522A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.667A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.840A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 652 removed outlier: 3.586A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.688A pdb=" N LEU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 732 removed outlier: 3.935A pdb=" N ILE A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.858A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 804 removed outlier: 3.694A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'O' and resid 9 through 31 removed outlier: 3.829A pdb=" N CYS O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL O 15 " --> pdb=" O TRP O 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU O 16 " --> pdb=" O CYS O 12 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER O 17 " --> pdb=" O CYS O 13 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU O 24 " --> pdb=" O GLY O 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 27 " --> pdb=" O ILE O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 75 removed outlier: 4.343A pdb=" N VAL O 55 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE O 65 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN O 72 " --> pdb=" O PHE O 68 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL O 73 " --> pdb=" O CYS O 69 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 75 " --> pdb=" O PHE O 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.936A pdb=" N GLN A 40 " --> pdb=" O TRP A 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 338 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 334 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 329 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.936A pdb=" N GLN A 40 " --> pdb=" O TRP A 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 338 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 341 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 15 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 4.207A pdb=" N PHE A 212 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 379 1395 hydrogen bonds defined for protein. 4152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6511 1.34 - 1.46: 4887 1.46 - 1.58: 10956 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 22558 Sorted by residual: bond pdb=" C ALA D 15 " pdb=" N PRO D 16 " ideal model delta sigma weight residual 1.335 1.383 -0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" CB MET A 468 " pdb=" CG MET A 468 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 bond pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" C ASP O 44 " pdb=" N PRO O 45 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.55e+00 bond pdb=" CB VAL M 60 " pdb=" CG2 VAL M 60 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 ... (remaining 22553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 29484 2.40 - 4.80: 966 4.80 - 7.19: 142 7.19 - 9.59: 39 9.59 - 11.99: 7 Bond angle restraints: 30638 Sorted by residual: angle pdb=" C MET A 422 " pdb=" N PHE A 423 " pdb=" CA PHE A 423 " ideal model delta sigma weight residual 122.46 113.39 9.07 1.80e+00 3.09e-01 2.54e+01 angle pdb=" C GLN I 156 " pdb=" N ASP I 157 " pdb=" CA ASP I 157 " ideal model delta sigma weight residual 122.82 129.91 -7.09 1.42e+00 4.96e-01 2.50e+01 angle pdb=" C ASN A 384 " pdb=" N LYS A 385 " pdb=" CA LYS A 385 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 angle pdb=" CA THR N 250 " pdb=" CB THR N 250 " pdb=" CG2 THR N 250 " ideal model delta sigma weight residual 110.50 118.28 -7.78 1.70e+00 3.46e-01 2.09e+01 angle pdb=" N GLY A 524 " pdb=" CA GLY A 524 " pdb=" C GLY A 524 " ideal model delta sigma weight residual 112.49 117.79 -5.30 1.21e+00 6.83e-01 1.92e+01 ... (remaining 30633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 12218 16.14 - 32.28: 676 32.28 - 48.42: 202 48.42 - 64.57: 6 64.57 - 80.71: 10 Dihedral angle restraints: 13112 sinusoidal: 4829 harmonic: 8283 Sorted by residual: dihedral pdb=" CA GLU L 137 " pdb=" C GLU L 137 " pdb=" N VAL L 138 " pdb=" CA VAL L 138 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA MET A 422 " pdb=" C MET A 422 " pdb=" N PHE A 423 " pdb=" CA PHE A 423 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG B 276 " pdb=" C ARG B 276 " pdb=" N GLY B 277 " pdb=" CA GLY B 277 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 13109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2800 0.063 - 0.126: 705 0.126 - 0.189: 127 0.189 - 0.251: 12 0.251 - 0.314: 6 Chirality restraints: 3650 Sorted by residual: chirality pdb=" CB ILE N 218 " pdb=" CA ILE N 218 " pdb=" CG1 ILE N 218 " pdb=" CG2 ILE N 218 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU A 818 " pdb=" N GLU A 818 " pdb=" C GLU A 818 " pdb=" CB GLU A 818 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB ILE C 45 " pdb=" CA ILE C 45 " pdb=" CG1 ILE C 45 " pdb=" CG2 ILE C 45 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3647 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 200 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO B 201 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 102 " 0.018 2.00e-02 2.50e+03 1.83e-02 6.70e+00 pdb=" CG TYR B 102 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 102 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 102 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 102 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 102 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 102 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 423 " -0.021 2.00e-02 2.50e+03 1.85e-02 6.00e+00 pdb=" CG PHE A 423 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 423 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 423 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 423 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 423 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 423 " -0.001 2.00e-02 2.50e+03 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3933 2.76 - 3.29: 22511 3.29 - 3.83: 37010 3.83 - 4.36: 42844 4.36 - 4.90: 70870 Nonbonded interactions: 177168 Sorted by model distance: nonbonded pdb=" O VAL B 152 " pdb=" OG1 THR B 156 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP C 44 " pdb=" OG SER N 216 " model vdw 2.269 3.040 nonbonded pdb=" O ASP B 298 " pdb=" OG1 THR B 301 " model vdw 2.289 3.040 nonbonded pdb=" ND2 ASN A 480 " pdb=" O LEU A 518 " model vdw 2.295 3.120 ... (remaining 177163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 1 through 159) selection = chain 'I' selection = chain 'J' selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.006 0.088 22558 Z= 0.275 Angle : 1.033 11.988 30638 Z= 0.543 Chirality : 0.057 0.314 3650 Planarity : 0.006 0.067 3802 Dihedral : 11.468 80.707 7854 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.34 % Allowed : 6.02 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.12), residues: 2884 helix: -2.93 (0.08), residues: 1916 sheet: -0.23 (0.77), residues: 43 loop : -2.14 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 117 TYR 0.039 0.003 TYR A 300 PHE 0.041 0.003 PHE A 423 TRP 0.031 0.003 TRP C 77 HIS 0.016 0.002 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00639 (22558) covalent geometry : angle 1.03262 (30638) hydrogen bonds : bond 0.28110 ( 1393) hydrogen bonds : angle 9.42551 ( 4152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 652 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7986 (tt0) cc_final: 0.7770 (tm-30) REVERT: D 58 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7768 (mmmt) REVERT: D 59 SER cc_start: 0.8773 (t) cc_final: 0.8199 (p) REVERT: D 114 TYR cc_start: 0.8050 (t80) cc_final: 0.7844 (t80) REVERT: D 132 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7100 (tpp-160) REVERT: C 38 PHE cc_start: 0.8843 (m-10) cc_final: 0.8341 (m-80) REVERT: C 100 ASN cc_start: 0.9062 (t0) cc_final: 0.8766 (t0) REVERT: C 108 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 211 GLU cc_start: 0.8473 (pm20) cc_final: 0.8199 (pm20) REVERT: N 256 LYS cc_start: 0.7920 (tmtm) cc_final: 0.7358 (pptt) REVERT: N 259 ASN cc_start: 0.6633 (t0) cc_final: 0.5324 (m110) REVERT: M 43 MET cc_start: 0.7804 (mmt) cc_final: 0.7204 (mmt) REVERT: M 44 MET cc_start: 0.7496 (ttp) cc_final: 0.6999 (tpp) REVERT: E 47 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: E 85 TYR cc_start: 0.8540 (t80) cc_final: 0.8093 (t80) REVERT: E 130 ILE cc_start: 0.7409 (pp) cc_final: 0.7142 (mt) REVERT: B 128 HIS cc_start: 0.8042 (t70) cc_final: 0.7365 (t-170) REVERT: B 188 TYR cc_start: 0.7755 (t80) cc_final: 0.7524 (t80) REVERT: B 202 GLU cc_start: 0.8041 (tp30) cc_final: 0.7745 (tp30) REVERT: B 230 SER cc_start: 0.8562 (t) cc_final: 0.8245 (p) REVERT: B 280 GLU cc_start: 0.8475 (mp0) cc_final: 0.7730 (tp30) REVERT: B 328 GLU cc_start: 0.8173 (tt0) cc_final: 0.7860 (tm-30) REVERT: F 48 ASP cc_start: 0.8639 (m-30) cc_final: 0.8146 (p0) REVERT: F 52 LYS cc_start: 0.7660 (tppp) cc_final: 0.7364 (tptp) REVERT: F 121 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8383 (mp10) REVERT: F 124 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7811 (ttm170) REVERT: F 155 THR cc_start: 0.8067 (m) cc_final: 0.7702 (p) REVERT: G 48 ASP cc_start: 0.8391 (m-30) cc_final: 0.8165 (m-30) REVERT: G 52 LYS cc_start: 0.7394 (mmpt) cc_final: 0.7155 (mmtt) REVERT: G 122 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7995 (tp-100) REVERT: G 129 MET cc_start: 0.7423 (tmm) cc_final: 0.7095 (tmm) REVERT: G 137 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7374 (tm-30) REVERT: G 139 LEU cc_start: 0.8336 (mp) cc_final: 0.8071 (tt) REVERT: G 156 GLN cc_start: 0.7436 (pp30) cc_final: 0.7179 (pp30) REVERT: H 43 CYS cc_start: 0.8481 (m) cc_final: 0.8271 (m) REVERT: H 85 TYR cc_start: 0.8562 (t80) cc_final: 0.8336 (t80) REVERT: I 3 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7680 (pm20) REVERT: I 50 LEU cc_start: 0.7854 (pt) cc_final: 0.6692 (tp) REVERT: I 51 PHE cc_start: 0.8718 (m-80) cc_final: 0.7821 (t80) REVERT: I 55 VAL cc_start: 0.7894 (m) cc_final: 0.7571 (t) REVERT: I 76 TYR cc_start: 0.8511 (m-80) cc_final: 0.8162 (m-80) REVERT: I 80 GLN cc_start: 0.8991 (pm20) cc_final: 0.8651 (tt0) REVERT: I 81 LYS cc_start: 0.9214 (mttm) cc_final: 0.8782 (mmmt) REVERT: J 47 PRO cc_start: 0.8448 (Cg_endo) cc_final: 0.8024 (Cg_exo) REVERT: J 48 ASP cc_start: 0.8911 (m-30) cc_final: 0.8635 (t0) REVERT: J 52 LYS cc_start: 0.8057 (tttt) cc_final: 0.7790 (tptt) REVERT: K 46 ARG cc_start: 0.8031 (ttt180) cc_final: 0.7795 (mtp180) REVERT: K 153 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7098 (ttm-80) REVERT: K 157 ASP cc_start: 0.8271 (t0) cc_final: 0.7635 (t0) REVERT: L 121 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8386 (mm-40) REVERT: L 137 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 130 GLN cc_start: 0.7105 (tt0) cc_final: 0.6739 (tm-30) REVERT: A 200 GLU cc_start: 0.8852 (tp30) cc_final: 0.8603 (tp30) REVERT: A 223 TYR cc_start: 0.7786 (m-10) cc_final: 0.7584 (m-80) REVERT: A 254 GLU cc_start: 0.8924 (tt0) cc_final: 0.8281 (tp30) REVERT: A 270 ARG cc_start: 0.6527 (ttp80) cc_final: 0.6135 (ttm110) REVERT: A 287 VAL cc_start: 0.7932 (m) cc_final: 0.7726 (p) REVERT: A 338 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8209 (mt-10) REVERT: A 489 ILE cc_start: 0.7894 (tp) cc_final: 0.7641 (tt) REVERT: A 504 GLU cc_start: 0.8181 (tt0) cc_final: 0.7980 (tt0) REVERT: A 764 PHE cc_start: 0.4968 (t80) cc_final: 0.4349 (m-80) REVERT: A 769 MET cc_start: 0.8338 (tpp) cc_final: 0.8086 (ttm) REVERT: A 776 MET cc_start: 0.6910 (mtt) cc_final: 0.6555 (tpp) REVERT: A 788 MET cc_start: 0.7847 (mmp) cc_final: 0.7642 (tpp) REVERT: A 817 TYR cc_start: 0.7612 (t80) cc_final: 0.7312 (t80) REVERT: A 823 GLU cc_start: 0.8611 (tt0) cc_final: 0.8252 (mp0) REVERT: O 14 THR cc_start: 0.6839 (m) cc_final: 0.6421 (p) REVERT: O 36 GLU cc_start: 0.7977 (pt0) cc_final: 0.7303 (pp20) REVERT: O 65 PHE cc_start: 0.7944 (m-80) cc_final: 0.7730 (m-10) REVERT: O 72 GLN cc_start: 0.7827 (pt0) cc_final: 0.7278 (pp30) outliers start: 8 outliers final: 1 residues processed: 659 average time/residue: 0.1649 time to fit residues: 167.8146 Evaluate side-chains 404 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 403 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 156 GLN B 128 HIS F 90 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 151 ASN J 80 GLN J 90 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 391 GLN A 547 HIS A 745 GLN A 756 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.129390 restraints weight = 37975.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133034 restraints weight = 16166.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135331 restraints weight = 8662.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136687 restraints weight = 5514.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.137689 restraints weight = 4075.874| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22558 Z= 0.155 Angle : 0.685 9.861 30638 Z= 0.354 Chirality : 0.041 0.188 3650 Planarity : 0.005 0.062 3802 Dihedral : 5.201 33.280 3117 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.59 % Allowed : 13.62 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.14), residues: 2884 helix: -1.14 (0.10), residues: 2046 sheet: 0.22 (0.74), residues: 43 loop : -2.18 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 46 TYR 0.020 0.001 TYR D 72 PHE 0.029 0.002 PHE A 423 TRP 0.019 0.002 TRP A 751 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00331 (22558) covalent geometry : angle 0.68467 (30638) hydrogen bonds : bond 0.05743 ( 1393) hydrogen bonds : angle 4.92589 ( 4152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 485 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 129 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8225 (p) REVERT: C 181 PHE cc_start: 0.7234 (t80) cc_final: 0.7009 (t80) REVERT: C 185 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6902 (mt) REVERT: N 259 ASN cc_start: 0.5747 (t0) cc_final: 0.5208 (m110) REVERT: M 51 THR cc_start: 0.9205 (t) cc_final: 0.8892 (t) REVERT: E 85 TYR cc_start: 0.8111 (t80) cc_final: 0.7827 (t80) REVERT: E 152 SER cc_start: 0.8075 (t) cc_final: 0.7455 (m) REVERT: B 153 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6872 (tp) REVERT: B 178 GLU cc_start: 0.7924 (tp30) cc_final: 0.7709 (mt-10) REVERT: B 230 SER cc_start: 0.8423 (t) cc_final: 0.8132 (p) REVERT: F 110 ILE cc_start: 0.8977 (tp) cc_final: 0.8653 (tp) REVERT: G 129 MET cc_start: 0.8103 (tmm) cc_final: 0.7847 (ttp) REVERT: G 151 ASN cc_start: 0.8730 (t0) cc_final: 0.8389 (t0) REVERT: H 85 TYR cc_start: 0.8282 (t80) cc_final: 0.8005 (t80) REVERT: H 149 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8386 (tt) REVERT: I 30 TYR cc_start: 0.8101 (t80) cc_final: 0.7855 (t80) REVERT: I 50 LEU cc_start: 0.7724 (pt) cc_final: 0.6565 (tp) REVERT: I 51 PHE cc_start: 0.7911 (m-80) cc_final: 0.7540 (t80) REVERT: I 81 LYS cc_start: 0.8685 (mttm) cc_final: 0.8294 (mmmt) REVERT: J 52 LYS cc_start: 0.7764 (tttt) cc_final: 0.7536 (tptt) REVERT: K 73 LEU cc_start: 0.8988 (tp) cc_final: 0.8761 (tp) REVERT: K 157 ASP cc_start: 0.8073 (t0) cc_final: 0.7715 (t0) REVERT: L 53 ASN cc_start: 0.8589 (m-40) cc_final: 0.8143 (t0) REVERT: L 75 CYS cc_start: 0.8380 (t) cc_final: 0.8137 (m) REVERT: L 121 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7663 (mm-40) REVERT: A 254 GLU cc_start: 0.8820 (tt0) cc_final: 0.8377 (tp30) REVERT: A 287 VAL cc_start: 0.8369 (m) cc_final: 0.7963 (p) REVERT: A 481 ASP cc_start: 0.7549 (m-30) cc_final: 0.7175 (t0) REVERT: A 613 ILE cc_start: 0.8413 (pt) cc_final: 0.8206 (mm) REVERT: A 721 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7351 (tt0) REVERT: A 764 PHE cc_start: 0.4385 (t80) cc_final: 0.3879 (m-80) REVERT: A 769 MET cc_start: 0.7954 (tpp) cc_final: 0.7672 (ttm) REVERT: A 780 LEU cc_start: 0.8248 (mm) cc_final: 0.7656 (mm) REVERT: O 4 VAL cc_start: 0.1857 (OUTLIER) cc_final: 0.1471 (t) REVERT: O 36 GLU cc_start: 0.7554 (pt0) cc_final: 0.7166 (pp20) outliers start: 84 outliers final: 40 residues processed: 541 average time/residue: 0.1394 time to fit residues: 122.8761 Evaluate side-chains 424 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 63 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 171 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN E 53 ASN E 90 GLN B 258 GLN F 53 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.146018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128113 restraints weight = 36764.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131877 restraints weight = 15626.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134265 restraints weight = 8326.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135700 restraints weight = 5267.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136596 restraints weight = 3841.927| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22558 Z= 0.142 Angle : 0.648 10.907 30638 Z= 0.329 Chirality : 0.040 0.199 3650 Planarity : 0.004 0.053 3802 Dihedral : 4.762 19.221 3115 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.87 % Allowed : 15.96 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2884 helix: -0.34 (0.11), residues: 2015 sheet: 0.88 (0.85), residues: 37 loop : -1.87 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 153 TYR 0.018 0.001 TYR N 251 PHE 0.025 0.001 PHE K 88 TRP 0.014 0.001 TRP A 751 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00311 (22558) covalent geometry : angle 0.64756 (30638) hydrogen bonds : bond 0.04746 ( 1393) hydrogen bonds : angle 4.40109 ( 4152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 425 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7895 (tpp80) REVERT: D 127 TYR cc_start: 0.7124 (t80) cc_final: 0.6864 (t80) REVERT: D 145 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 129 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 183 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7716 (tptt) REVERT: N 259 ASN cc_start: 0.5768 (t0) cc_final: 0.5170 (m110) REVERT: M 43 MET cc_start: 0.7902 (mmt) cc_final: 0.7012 (mmt) REVERT: M 51 THR cc_start: 0.9222 (t) cc_final: 0.8917 (t) REVERT: B 230 SER cc_start: 0.8455 (t) cc_final: 0.8107 (p) REVERT: B 236 ASP cc_start: 0.7297 (m-30) cc_final: 0.7061 (t0) REVERT: B 280 GLU cc_start: 0.7548 (mp0) cc_final: 0.6906 (tm-30) REVERT: G 45 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7489 (mt) REVERT: G 59 MET cc_start: 0.7277 (mtt) cc_final: 0.7053 (mtt) REVERT: H 90 GLN cc_start: 0.8626 (mt0) cc_final: 0.8309 (mt0) REVERT: H 149 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8418 (tt) REVERT: I 30 TYR cc_start: 0.8110 (t80) cc_final: 0.7816 (t80) REVERT: I 50 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7376 (tp) REVERT: I 81 LYS cc_start: 0.8588 (mttm) cc_final: 0.8375 (mmmt) REVERT: J 47 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.8124 (Cg_endo) REVERT: J 52 LYS cc_start: 0.7718 (tttt) cc_final: 0.7420 (tptt) REVERT: K 153 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7350 (ttm-80) REVERT: K 157 ASP cc_start: 0.8055 (t0) cc_final: 0.7601 (t0) REVERT: L 75 CYS cc_start: 0.8280 (t) cc_final: 0.8035 (t) REVERT: L 121 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7644 (mm-40) REVERT: L 126 PHE cc_start: 0.8194 (t80) cc_final: 0.7865 (t80) REVERT: L 129 MET cc_start: 0.8363 (tmm) cc_final: 0.7997 (tmm) REVERT: A 124 MET cc_start: 0.8617 (mmm) cc_final: 0.8329 (mmm) REVERT: A 254 GLU cc_start: 0.8779 (tt0) cc_final: 0.8261 (tp30) REVERT: A 422 MET cc_start: 0.8115 (mmm) cc_final: 0.7898 (mmt) REVERT: A 481 ASP cc_start: 0.7533 (m-30) cc_final: 0.7096 (t0) REVERT: A 543 MET cc_start: 0.7550 (tmm) cc_final: 0.7326 (tmm) REVERT: A 565 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7036 (ppp) REVERT: A 721 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7408 (tt0) REVERT: A 769 MET cc_start: 0.8081 (tpp) cc_final: 0.7333 (ptt) REVERT: A 776 MET cc_start: 0.7869 (tpp) cc_final: 0.7457 (tpp) REVERT: A 780 LEU cc_start: 0.8199 (mm) cc_final: 0.7882 (mm) REVERT: A 788 MET cc_start: 0.6628 (tpp) cc_final: 0.6419 (tpp) outliers start: 114 outliers final: 66 residues processed: 502 average time/residue: 0.1333 time to fit residues: 111.0715 Evaluate side-chains 434 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 248 ASP Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 63 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 19 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 179 optimal weight: 0.0470 chunk 110 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN I 53 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN K 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.149087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.131047 restraints weight = 38121.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.134654 restraints weight = 16384.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136974 restraints weight = 8857.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.138291 restraints weight = 5690.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.139323 restraints weight = 4261.569| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22558 Z= 0.123 Angle : 0.619 10.474 30638 Z= 0.307 Chirality : 0.039 0.189 3650 Planarity : 0.004 0.050 3802 Dihedral : 4.522 18.184 3115 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.05 % Allowed : 19.50 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 2884 helix: 0.09 (0.11), residues: 2028 sheet: 1.11 (0.87), residues: 37 loop : -1.80 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.014 0.001 TYR A 328 PHE 0.023 0.001 PHE A 572 TRP 0.011 0.001 TRP A 751 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00260 (22558) covalent geometry : angle 0.61857 (30638) hydrogen bonds : bond 0.04149 ( 1393) hydrogen bonds : angle 4.10961 ( 4152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 426 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8170 (tt) REVERT: D 125 ARG cc_start: 0.8284 (tpp80) cc_final: 0.8080 (tpp80) REVERT: D 145 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 129 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8206 (p) REVERT: C 181 PHE cc_start: 0.7067 (t80) cc_final: 0.6779 (t80) REVERT: C 183 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8055 (tptt) REVERT: N 259 ASN cc_start: 0.5684 (t0) cc_final: 0.5170 (m110) REVERT: M 43 MET cc_start: 0.7910 (mmt) cc_final: 0.7101 (mmt) REVERT: M 46 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7158 (tt) REVERT: E 122 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7364 (tp40) REVERT: B 230 SER cc_start: 0.8291 (t) cc_final: 0.7984 (p) REVERT: B 280 GLU cc_start: 0.7519 (mp0) cc_final: 0.6958 (tm-30) REVERT: G 45 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7352 (mt) REVERT: G 59 MET cc_start: 0.7486 (mtt) cc_final: 0.7158 (mtt) REVERT: G 158 VAL cc_start: 0.7220 (t) cc_final: 0.6986 (p) REVERT: H 149 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8504 (tt) REVERT: I 30 TYR cc_start: 0.8143 (t80) cc_final: 0.7928 (t80) REVERT: I 50 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7350 (tp) REVERT: J 52 LYS cc_start: 0.7670 (tttt) cc_final: 0.7394 (tptt) REVERT: K 157 ASP cc_start: 0.7991 (t0) cc_final: 0.7474 (t0) REVERT: L 121 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7567 (mm-40) REVERT: L 129 MET cc_start: 0.8273 (tmm) cc_final: 0.7792 (tmm) REVERT: L 133 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 124 MET cc_start: 0.8530 (mmm) cc_final: 0.8279 (mmm) REVERT: A 254 GLU cc_start: 0.8736 (tt0) cc_final: 0.8164 (tp30) REVERT: A 405 ILE cc_start: 0.8580 (mm) cc_final: 0.8380 (mm) REVERT: A 454 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 472 SER cc_start: 0.8640 (t) cc_final: 0.7972 (p) REVERT: A 565 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7039 (ppp) REVERT: A 769 MET cc_start: 0.8062 (tpp) cc_final: 0.7344 (ptt) REVERT: A 776 MET cc_start: 0.7486 (tpp) cc_final: 0.7000 (tpp) REVERT: A 788 MET cc_start: 0.6557 (tpp) cc_final: 0.6247 (tpp) REVERT: O 19 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6468 (t80) REVERT: O 62 TYR cc_start: 0.7597 (m-80) cc_final: 0.7392 (m-80) outliers start: 95 outliers final: 54 residues processed: 487 average time/residue: 0.1412 time to fit residues: 112.9079 Evaluate side-chains 437 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 146 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.143771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126327 restraints weight = 37650.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129800 restraints weight = 16392.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132025 restraints weight = 8943.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133429 restraints weight = 5762.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134386 restraints weight = 4234.070| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22558 Z= 0.157 Angle : 0.649 10.191 30638 Z= 0.326 Chirality : 0.040 0.187 3650 Planarity : 0.004 0.059 3802 Dihedral : 4.507 18.040 3115 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.16 % Allowed : 19.89 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 2884 helix: 0.12 (0.11), residues: 2062 sheet: 0.93 (0.85), residues: 37 loop : -1.86 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 153 TYR 0.021 0.001 TYR E 85 PHE 0.029 0.002 PHE A 572 TRP 0.014 0.001 TRP A 647 HIS 0.010 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00361 (22558) covalent geometry : angle 0.64854 (30638) hydrogen bonds : bond 0.04274 ( 1393) hydrogen bonds : angle 4.16803 ( 4152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 381 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 129 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8247 (p) REVERT: C 181 PHE cc_start: 0.7094 (t80) cc_final: 0.6854 (t80) REVERT: C 183 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7921 (tptm) REVERT: N 259 ASN cc_start: 0.5492 (t0) cc_final: 0.5191 (m110) REVERT: M 43 MET cc_start: 0.8012 (mmt) cc_final: 0.7137 (mmt) REVERT: M 46 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7258 (tt) REVERT: M 66 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: E 106 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: E 122 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7434 (tp-100) REVERT: E 157 ASP cc_start: 0.7444 (t70) cc_final: 0.7158 (t0) REVERT: B 230 SER cc_start: 0.8309 (t) cc_final: 0.7992 (p) REVERT: F 110 ILE cc_start: 0.9000 (tp) cc_final: 0.8793 (tp) REVERT: G 45 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7500 (mt) REVERT: G 122 GLN cc_start: 0.8359 (tp-100) cc_final: 0.7376 (tm-30) REVERT: H 149 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8515 (tt) REVERT: I 30 TYR cc_start: 0.8169 (t80) cc_final: 0.7924 (t80) REVERT: I 50 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7186 (tp) REVERT: K 137 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7672 (tm-30) REVERT: K 153 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.7089 (ttm-80) REVERT: K 157 ASP cc_start: 0.8097 (t0) cc_final: 0.7720 (t0) REVERT: L 121 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7657 (mm-40) REVERT: L 126 PHE cc_start: 0.8316 (t80) cc_final: 0.8103 (t80) REVERT: L 129 MET cc_start: 0.8354 (tmm) cc_final: 0.7913 (tmm) REVERT: L 133 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8696 (tt) REVERT: A 124 MET cc_start: 0.8590 (mmm) cc_final: 0.8331 (mmm) REVERT: A 323 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7739 (tt) REVERT: A 565 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7047 (ppp) REVERT: A 721 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7393 (tt0) REVERT: A 769 MET cc_start: 0.8143 (tpp) cc_final: 0.7375 (ptt) REVERT: A 776 MET cc_start: 0.7533 (tpp) cc_final: 0.7121 (tpp) REVERT: A 780 LEU cc_start: 0.8487 (mt) cc_final: 0.8010 (mp) REVERT: A 788 MET cc_start: 0.6838 (tpp) cc_final: 0.6557 (tpp) outliers start: 121 outliers final: 84 residues processed: 467 average time/residue: 0.1375 time to fit residues: 106.1927 Evaluate side-chains 444 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 350 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 226 CYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 106 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 311 GLN A 547 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 745 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.140513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.123112 restraints weight = 38503.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126508 restraints weight = 16756.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.128724 restraints weight = 9209.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130132 restraints weight = 5908.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131067 restraints weight = 4323.223| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22558 Z= 0.177 Angle : 0.679 11.501 30638 Z= 0.342 Chirality : 0.041 0.197 3650 Planarity : 0.004 0.046 3802 Dihedral : 4.615 19.174 3115 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.38 % Allowed : 20.83 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2884 helix: 0.08 (0.11), residues: 2061 sheet: 0.91 (0.74), residues: 43 loop : -1.89 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 153 TYR 0.021 0.002 TYR N 251 PHE 0.024 0.002 PHE C 38 TRP 0.016 0.002 TRP A 647 HIS 0.009 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00409 (22558) covalent geometry : angle 0.67898 (30638) hydrogen bonds : bond 0.04500 ( 1393) hydrogen bonds : angle 4.27872 ( 4152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 389 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7411 (tp30) REVERT: D 145 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 129 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8237 (p) REVERT: N 259 ASN cc_start: 0.5922 (t0) cc_final: 0.5615 (m110) REVERT: M 43 MET cc_start: 0.8116 (mmt) cc_final: 0.7310 (mmt) REVERT: M 66 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: E 88 PHE cc_start: 0.7826 (m-80) cc_final: 0.7249 (m-80) REVERT: E 106 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6772 (m-10) REVERT: E 122 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7383 (mm-40) REVERT: E 157 ASP cc_start: 0.7348 (t70) cc_final: 0.7013 (t0) REVERT: B 229 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7687 (mt0) REVERT: B 280 GLU cc_start: 0.7917 (mp0) cc_final: 0.7360 (tm-30) REVERT: F 15 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7810 (tp) REVERT: F 53 ASN cc_start: 0.8248 (t0) cc_final: 0.7727 (t0) REVERT: G 45 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7483 (mt) REVERT: G 59 MET cc_start: 0.7309 (mtt) cc_final: 0.7076 (mtt) REVERT: H 149 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (tt) REVERT: I 30 TYR cc_start: 0.8248 (t80) cc_final: 0.7852 (t80) REVERT: I 49 LEU cc_start: 0.7199 (tp) cc_final: 0.6913 (tp) REVERT: I 50 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7056 (tp) REVERT: I 51 PHE cc_start: 0.7631 (m-80) cc_final: 0.7383 (m-80) REVERT: K 137 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7684 (tm-30) REVERT: K 153 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7137 (ttm-80) REVERT: K 157 ASP cc_start: 0.8219 (t0) cc_final: 0.7757 (t0) REVERT: L 121 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7677 (mm-40) REVERT: L 129 MET cc_start: 0.8471 (tmm) cc_final: 0.7945 (tmm) REVERT: A 124 MET cc_start: 0.8562 (mmm) cc_final: 0.8307 (mmm) REVERT: A 203 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 776 MET cc_start: 0.7233 (tpp) cc_final: 0.6973 (tpp) REVERT: A 780 LEU cc_start: 0.8471 (mt) cc_final: 0.7873 (mp) REVERT: A 788 MET cc_start: 0.6787 (tpp) cc_final: 0.6553 (tpp) outliers start: 126 outliers final: 86 residues processed: 477 average time/residue: 0.1416 time to fit residues: 111.2883 Evaluate side-chains 452 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 358 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 236 ILE Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 151 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.145984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.128405 restraints weight = 37859.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132017 restraints weight = 16061.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.134350 restraints weight = 8565.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135789 restraints weight = 5405.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136761 restraints weight = 3913.140| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22558 Z= 0.124 Angle : 0.637 10.097 30638 Z= 0.314 Chirality : 0.039 0.218 3650 Planarity : 0.004 0.048 3802 Dihedral : 4.432 24.246 3115 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.67 % Allowed : 23.60 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2884 helix: 0.33 (0.12), residues: 2036 sheet: 1.01 (0.75), residues: 43 loop : -1.80 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 63 TYR 0.025 0.001 TYR B 100 PHE 0.026 0.001 PHE H 88 TRP 0.009 0.001 TRP A 494 HIS 0.006 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00268 (22558) covalent geometry : angle 0.63655 (30638) hydrogen bonds : bond 0.03962 ( 1393) hydrogen bonds : angle 4.04499 ( 4152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 405 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8248 (tt) REVERT: D 145 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 129 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8226 (p) REVERT: C 183 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7582 (tptm) REVERT: N 259 ASN cc_start: 0.6047 (t0) cc_final: 0.5685 (m110) REVERT: M 43 MET cc_start: 0.8084 (mmt) cc_final: 0.7313 (mmt) REVERT: E 59 MET cc_start: 0.7691 (tpp) cc_final: 0.7420 (tpp) REVERT: E 106 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6743 (m-10) REVERT: E 122 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7176 (tp-100) REVERT: E 157 ASP cc_start: 0.7273 (t70) cc_final: 0.6977 (t0) REVERT: B 229 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7490 (mt0) REVERT: B 280 GLU cc_start: 0.7841 (mp0) cc_final: 0.7222 (tm-30) REVERT: F 91 LEU cc_start: 0.7052 (tt) cc_final: 0.6611 (tp) REVERT: F 110 ILE cc_start: 0.9028 (tp) cc_final: 0.8822 (tp) REVERT: G 45 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7248 (mt) REVERT: G 122 GLN cc_start: 0.8410 (tp-100) cc_final: 0.7521 (tm-30) REVERT: G 142 TYR cc_start: 0.7693 (m-80) cc_final: 0.7319 (m-80) REVERT: H 149 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8518 (tt) REVERT: I 30 TYR cc_start: 0.8150 (t80) cc_final: 0.7841 (t80) REVERT: I 50 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6977 (tp) REVERT: I 51 PHE cc_start: 0.7658 (m-80) cc_final: 0.7406 (m-10) REVERT: I 144 LEU cc_start: 0.7812 (tt) cc_final: 0.7605 (tt) REVERT: K 153 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7065 (ttm-80) REVERT: K 157 ASP cc_start: 0.8118 (t0) cc_final: 0.7740 (t0) REVERT: L 121 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7720 (mm110) REVERT: L 129 MET cc_start: 0.8354 (tmm) cc_final: 0.8029 (tmm) REVERT: L 133 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 108 ASP cc_start: 0.8658 (t0) cc_final: 0.8418 (t0) REVERT: A 124 MET cc_start: 0.8584 (mmm) cc_final: 0.8298 (mmm) REVERT: A 203 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 211 LEU cc_start: 0.7769 (pt) cc_final: 0.7494 (pp) REVERT: A 472 SER cc_start: 0.8660 (t) cc_final: 0.8038 (p) REVERT: A 721 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7295 (tt0) REVERT: A 776 MET cc_start: 0.7138 (tpp) cc_final: 0.6881 (tpp) REVERT: A 780 LEU cc_start: 0.8492 (mt) cc_final: 0.8185 (mm) REVERT: A 788 MET cc_start: 0.6700 (tpp) cc_final: 0.6477 (tpp) outliers start: 86 outliers final: 55 residues processed: 458 average time/residue: 0.1360 time to fit residues: 103.1527 Evaluate side-chains 442 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 379 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 150 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 42 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: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.122179 restraints weight = 38596.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125571 restraints weight = 16904.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127695 restraints weight = 9258.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.129084 restraints weight = 6059.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129942 restraints weight = 4468.612| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 22558 Z= 0.196 Angle : 0.708 10.002 30638 Z= 0.355 Chirality : 0.043 0.292 3650 Planarity : 0.004 0.054 3802 Dihedral : 4.633 26.335 3115 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.52 % Allowed : 23.47 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 2884 helix: 0.13 (0.11), residues: 2054 sheet: 1.04 (0.74), residues: 43 loop : -1.89 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 63 TYR 0.025 0.002 TYR E 85 PHE 0.024 0.002 PHE H 88 TRP 0.020 0.002 TRP A 647 HIS 0.007 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00459 (22558) covalent geometry : angle 0.70782 (30638) hydrogen bonds : bond 0.04511 ( 1393) hydrogen bonds : angle 4.32315 ( 4152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 374 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 129 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (p) REVERT: C 181 PHE cc_start: 0.7271 (t80) cc_final: 0.6977 (t80) REVERT: C 183 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7703 (tptm) REVERT: N 259 ASN cc_start: 0.6572 (t0) cc_final: 0.6166 (m-40) REVERT: M 43 MET cc_start: 0.8237 (mmt) cc_final: 0.7404 (mmt) REVERT: E 59 MET cc_start: 0.7793 (tpp) cc_final: 0.7479 (tpp) REVERT: E 122 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7198 (mm-40) REVERT: E 157 ASP cc_start: 0.7341 (t70) cc_final: 0.6999 (t0) REVERT: B 229 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7508 (mt0) REVERT: B 280 GLU cc_start: 0.8031 (mp0) cc_final: 0.7171 (tm-30) REVERT: F 15 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7917 (tp) REVERT: F 53 ASN cc_start: 0.8212 (t0) cc_final: 0.7837 (t0) REVERT: G 45 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7407 (mt) REVERT: G 59 MET cc_start: 0.6936 (mtt) cc_final: 0.6720 (mtt) REVERT: G 129 MET cc_start: 0.8251 (ttp) cc_final: 0.8020 (ttp) REVERT: H 149 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8527 (tt) REVERT: I 50 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.6848 (tp) REVERT: I 51 PHE cc_start: 0.7722 (m-80) cc_final: 0.7300 (m-10) REVERT: J 121 GLN cc_start: 0.7602 (mp-120) cc_final: 0.7282 (mm-40) REVERT: K 137 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7661 (tm-30) REVERT: K 153 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7068 (ttm-80) REVERT: K 157 ASP cc_start: 0.8211 (t0) cc_final: 0.7845 (t0) REVERT: L 75 CYS cc_start: 0.8184 (t) cc_final: 0.7270 (t) REVERT: L 121 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7611 (mm-40) REVERT: L 129 MET cc_start: 0.8442 (tmm) cc_final: 0.8073 (tmm) REVERT: A 124 MET cc_start: 0.8606 (mmm) cc_final: 0.8360 (mmm) REVERT: A 203 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 211 LEU cc_start: 0.8012 (pt) cc_final: 0.7776 (pp) REVERT: A 257 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: A 721 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7468 (tt0) REVERT: A 780 LEU cc_start: 0.8466 (mt) cc_final: 0.7748 (mp) REVERT: A 788 MET cc_start: 0.6803 (tpp) cc_final: 0.6591 (tpp) outliers start: 106 outliers final: 85 residues processed: 445 average time/residue: 0.1386 time to fit residues: 103.2498 Evaluate side-chains 454 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 362 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 168 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127273 restraints weight = 37967.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.130741 restraints weight = 16386.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.132984 restraints weight = 8878.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.134366 restraints weight = 5686.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.135269 restraints weight = 4179.278| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22558 Z= 0.129 Angle : 0.657 10.492 30638 Z= 0.321 Chirality : 0.040 0.268 3650 Planarity : 0.004 0.045 3802 Dihedral : 4.455 25.408 3115 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.46 % Allowed : 24.37 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2884 helix: 0.33 (0.12), residues: 2055 sheet: 1.14 (0.76), residues: 43 loop : -1.85 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 153 TYR 0.021 0.001 TYR E 85 PHE 0.019 0.001 PHE H 106 TRP 0.015 0.001 TRP A 647 HIS 0.006 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00285 (22558) covalent geometry : angle 0.65708 (30638) hydrogen bonds : bond 0.04005 ( 1393) hydrogen bonds : angle 4.08597 ( 4152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 388 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8153 (tt) REVERT: D 145 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 183 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7550 (tptt) REVERT: C 185 LEU cc_start: 0.7340 (mt) cc_final: 0.6990 (pp) REVERT: N 259 ASN cc_start: 0.6652 (t0) cc_final: 0.6305 (m-40) REVERT: M 43 MET cc_start: 0.8119 (mmt) cc_final: 0.7211 (mmt) REVERT: E 59 MET cc_start: 0.7679 (tpp) cc_final: 0.7265 (tpp) REVERT: E 122 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7195 (tp-100) REVERT: E 157 ASP cc_start: 0.7210 (t70) cc_final: 0.6881 (t0) REVERT: B 155 ASP cc_start: 0.7215 (m-30) cc_final: 0.6951 (t0) REVERT: B 229 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7444 (mt0) REVERT: B 280 GLU cc_start: 0.8005 (mp0) cc_final: 0.7230 (tm-30) REVERT: F 15 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7726 (tp) REVERT: F 53 ASN cc_start: 0.7703 (t0) cc_final: 0.7459 (t0) REVERT: F 91 LEU cc_start: 0.7268 (tt) cc_final: 0.6736 (tp) REVERT: F 110 ILE cc_start: 0.9053 (tp) cc_final: 0.8827 (tp) REVERT: F 121 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7312 (mm-40) REVERT: G 45 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7406 (mt) REVERT: G 59 MET cc_start: 0.6779 (mtt) cc_final: 0.6483 (mtt) REVERT: G 129 MET cc_start: 0.8087 (ttp) cc_final: 0.7751 (ttp) REVERT: G 142 TYR cc_start: 0.7688 (m-80) cc_final: 0.7347 (m-80) REVERT: H 149 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8492 (tt) REVERT: I 30 TYR cc_start: 0.8257 (t80) cc_final: 0.7881 (t80) REVERT: I 50 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.6777 (tp) REVERT: I 51 PHE cc_start: 0.7801 (m-80) cc_final: 0.7411 (m-10) REVERT: J 121 GLN cc_start: 0.7503 (mp-120) cc_final: 0.7222 (mm-40) REVERT: K 153 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7127 (ttm-80) REVERT: K 157 ASP cc_start: 0.8206 (t0) cc_final: 0.7783 (t0) REVERT: L 121 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7757 (mm110) REVERT: L 129 MET cc_start: 0.8297 (tmm) cc_final: 0.7960 (tmm) REVERT: A 77 LYS cc_start: 0.8720 (mmpt) cc_final: 0.8203 (tptm) REVERT: A 124 MET cc_start: 0.8573 (mmm) cc_final: 0.8304 (mmm) REVERT: A 203 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8735 (tt) REVERT: A 211 LEU cc_start: 0.7881 (pt) cc_final: 0.7643 (pp) REVERT: A 257 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6681 (m-30) REVERT: A 418 MET cc_start: 0.8387 (tpp) cc_final: 0.7900 (mmt) REVERT: A 472 SER cc_start: 0.8661 (t) cc_final: 0.8044 (p) REVERT: A 627 TYR cc_start: 0.5510 (t80) cc_final: 0.5229 (t80) REVERT: A 721 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7416 (tt0) REVERT: A 780 LEU cc_start: 0.8431 (mt) cc_final: 0.8195 (mp) REVERT: A 788 MET cc_start: 0.6705 (tpp) cc_final: 0.6473 (tpp) REVERT: A 797 SER cc_start: 0.8445 (t) cc_final: 0.8190 (t) outliers start: 81 outliers final: 64 residues processed: 440 average time/residue: 0.1369 time to fit residues: 100.1143 Evaluate side-chains 446 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 374 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 240 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 90 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.145482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.128097 restraints weight = 38037.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131520 restraints weight = 16442.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.133780 restraints weight = 9000.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.135181 restraints weight = 5768.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136132 restraints weight = 4233.368| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22558 Z= 0.127 Angle : 0.655 10.756 30638 Z= 0.318 Chirality : 0.040 0.282 3650 Planarity : 0.004 0.054 3802 Dihedral : 4.377 26.281 3115 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.24 % Allowed : 24.93 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2884 helix: 0.42 (0.12), residues: 2035 sheet: 1.18 (0.76), residues: 43 loop : -1.78 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 153 TYR 0.020 0.001 TYR D 72 PHE 0.034 0.001 PHE H 88 TRP 0.028 0.001 TRP A 777 HIS 0.007 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00279 (22558) covalent geometry : angle 0.65484 (30638) hydrogen bonds : bond 0.03887 ( 1393) hydrogen bonds : angle 4.02929 ( 4152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 398 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: D 74 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8248 (tt) REVERT: D 145 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 174 ASP cc_start: 0.8455 (t0) cc_final: 0.8209 (t0) REVERT: C 183 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7535 (tptt) REVERT: C 185 LEU cc_start: 0.7221 (mt) cc_final: 0.6850 (pp) REVERT: N 234 LEU cc_start: 0.9124 (tt) cc_final: 0.8921 (tt) REVERT: N 259 ASN cc_start: 0.6701 (t0) cc_final: 0.6345 (m-40) REVERT: E 59 MET cc_start: 0.7611 (tpp) cc_final: 0.7188 (tpp) REVERT: E 122 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7057 (tp-100) REVERT: E 157 ASP cc_start: 0.7250 (t70) cc_final: 0.6962 (t0) REVERT: B 155 ASP cc_start: 0.7058 (m-30) cc_final: 0.6805 (t0) REVERT: B 229 GLN cc_start: 0.8607 (tm-30) cc_final: 0.7375 (mt0) REVERT: B 280 GLU cc_start: 0.7972 (mp0) cc_final: 0.7249 (tm-30) REVERT: B 313 MET cc_start: 0.7651 (tpp) cc_final: 0.7397 (tpp) REVERT: F 15 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7719 (tp) REVERT: F 91 LEU cc_start: 0.7435 (tt) cc_final: 0.6911 (tp) REVERT: F 121 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7256 (mm-40) REVERT: G 45 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7421 (mt) REVERT: G 59 MET cc_start: 0.6657 (mtt) cc_final: 0.6405 (mtt) REVERT: G 129 MET cc_start: 0.8103 (ttp) cc_final: 0.7856 (ttp) REVERT: G 142 TYR cc_start: 0.7661 (m-80) cc_final: 0.7323 (m-80) REVERT: H 129 MET cc_start: 0.7648 (tmm) cc_final: 0.7187 (tmm) REVERT: H 149 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8477 (tt) REVERT: I 30 TYR cc_start: 0.8193 (t80) cc_final: 0.7879 (t80) REVERT: I 50 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.6760 (tp) REVERT: I 51 PHE cc_start: 0.7832 (m-80) cc_final: 0.7449 (m-10) REVERT: J 121 GLN cc_start: 0.7487 (mp-120) cc_final: 0.7270 (mm-40) REVERT: K 153 ARG cc_start: 0.7326 (ttm-80) cc_final: 0.7052 (ttm-80) REVERT: K 157 ASP cc_start: 0.8232 (t0) cc_final: 0.7788 (t0) REVERT: L 121 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7756 (mm110) REVERT: L 129 MET cc_start: 0.8307 (tmm) cc_final: 0.7962 (tmm) REVERT: A 77 LYS cc_start: 0.8604 (mmpt) cc_final: 0.8223 (tptm) REVERT: A 108 ASP cc_start: 0.8720 (t0) cc_final: 0.8488 (t0) REVERT: A 124 MET cc_start: 0.8572 (mmm) cc_final: 0.8353 (mmm) REVERT: A 203 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 211 LEU cc_start: 0.7950 (pt) cc_final: 0.7710 (pp) REVERT: A 472 SER cc_start: 0.8651 (t) cc_final: 0.8031 (p) REVERT: A 721 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7443 (tt0) REVERT: A 797 SER cc_start: 0.8456 (t) cc_final: 0.8236 (t) outliers start: 76 outliers final: 65 residues processed: 441 average time/residue: 0.1339 time to fit residues: 98.5992 Evaluate side-chains 452 residues out of total 2357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 126 PHE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.141837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124268 restraints weight = 38401.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127768 restraints weight = 16462.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.129996 restraints weight = 8891.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131289 restraints weight = 5731.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132337 restraints weight = 4284.183| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22558 Z= 0.167 Angle : 0.698 10.381 30638 Z= 0.346 Chirality : 0.042 0.284 3650 Planarity : 0.004 0.051 3802 Dihedral : 4.485 27.002 3115 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.46 % Allowed : 25.14 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2884 helix: 0.30 (0.12), residues: 2048 sheet: 1.20 (0.76), residues: 43 loop : -1.87 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 153 TYR 0.019 0.001 TYR E 85 PHE 0.032 0.002 PHE H 88 TRP 0.029 0.002 TRP A 777 HIS 0.008 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00388 (22558) covalent geometry : angle 0.69836 (30638) hydrogen bonds : bond 0.04197 ( 1393) hydrogen bonds : angle 4.21105 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3606.35 seconds wall clock time: 63 minutes 16.94 seconds (3796.94 seconds total)