Starting phenix.real_space_refine on Sat Jul 4 12:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.map" model { file = "/net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k29_36835/07_2026/8k29_36835.cif" } resolution = 3.18 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= 0.007 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 127 5.49 5 S 73 5.16 5 C 12855 2.51 5 N 3587 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 16, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "A" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1390 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 898 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "R" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 3.34, per 1000 atoms: 0.16 Number of scatterers: 21055 At special positions: 0 Unit cell: (113.3, 140.8, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 127 15.00 O 4413 8.00 N 3587 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 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 Atom "ATOM 19760 O5' DA Q 22 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 787.0 milliseconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 44 sheets defined 26.6% alpha, 22.1% beta 15 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.573A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.937A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.532A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.533A pdb=" N ASN B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.507A pdb=" N LEU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 150 through 155 removed outlier: 4.493A pdb=" N ASN B 153 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.806A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.510A pdb=" N ASN C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.524A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 284 through 298 removed outlier: 3.593A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.507A pdb=" N TRP D 130 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG D 131 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 133 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 134 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 4.070A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.558A pdb=" N LEU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 298 Processing helix chain 'E' and resid 99 through 107 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.841A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.510A pdb=" N LEU E 129 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 131 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 134 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.615A pdb=" N ASP E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.653A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 284 through 298 removed outlier: 3.567A pdb=" N PHE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 111 through 122 Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.685A pdb=" N TRP F 130 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG F 131 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.863A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.505A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 4.090A pdb=" N GLY F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.866A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.599A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 178 removed outlier: 3.549A pdb=" N VAL G 176 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.838A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 298 removed outlier: 3.703A pdb=" N PHE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.654A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.574A pdb=" N LEU H 129 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG H 131 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H 133 " --> pdb=" O TRP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 179 removed outlier: 4.163A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 285 through 298 Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 61 through 69 removed outlier: 4.153A pdb=" N LEU I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 109 removed outlier: 3.711A pdb=" N ARG I 103 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 removed outlier: 3.500A pdb=" N TYR I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA B 205 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU B 190 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 207 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS B 188 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 209 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 186 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 211 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 180 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 14 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.725A pdb=" N TYR C 12 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 26 current: chain 'C' and resid 139 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 85 current: chain 'C' and resid 217 through 218 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 45 removed outlier: 4.555A pdb=" N ALA C 68 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.575A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 139 through 144 Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 86 current: chain 'D' and resid 217 through 218 Processing sheet with id=AB9, first strand: chain 'D' and resid 40 through 45 Processing sheet with id=AC1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AC3, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 139 through 145 Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 86 current: chain 'E' and resid 217 through 218 Processing sheet with id=AC5, first strand: chain 'E' and resid 40 through 45 Processing sheet with id=AC6, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AC7, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.515A pdb=" N VAL E 255 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC9, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'F' and resid 39 through 46 Processing sheet with id=AD3, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.651A pdb=" N GLN F 214 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD5, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AD6, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.642A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.024A pdb=" N GLY G 299 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 139 through 144 Processing sheet with id=AD9, first strand: chain 'G' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 86 current: chain 'G' and resid 217 through 218 Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 44 removed outlier: 4.462A pdb=" N ALA G 68 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.582A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE4, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.568A pdb=" N MET H 191 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 145 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.580A pdb=" N MET H 224 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA H 222 " --> pdb=" O MET H 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 40 through 44 removed outlier: 3.867A pdb=" N GLY H 40 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 39 through 40 removed outlier: 5.999A pdb=" N THR I 3 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER I 5 " --> pdb=" O GLY I 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 90 through 93 removed outlier: 3.837A pdb=" N PHE I 147 " --> pdb=" O VAL I 93 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3338 1.30 - 1.43: 6164 1.43 - 1.56: 11796 1.56 - 1.69: 261 1.69 - 1.82: 131 Bond restraints: 21690 Sorted by residual: bond pdb=" CA LYS G 91 " pdb=" C LYS G 91 " ideal model delta sigma weight residual 1.523 1.414 0.108 1.23e-02 6.61e+03 7.77e+01 bond pdb=" CA ASP G 226 " pdb=" C ASP G 226 " ideal model delta sigma weight residual 1.522 1.419 0.104 1.37e-02 5.33e+03 5.71e+01 bond pdb=" CA THR A 99 " pdb=" C THR A 99 " ideal model delta sigma weight residual 1.525 1.442 0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" CA LYS G 228 " pdb=" C LYS G 228 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.29e-02 6.01e+03 3.56e+01 bond pdb=" CA HIS G 225 " pdb=" C HIS G 225 " ideal model delta sigma weight residual 1.527 1.452 0.075 1.34e-02 5.57e+03 3.10e+01 ... (remaining 21685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 29377 3.36 - 6.72: 500 6.72 - 10.09: 79 10.09 - 13.45: 11 13.45 - 16.81: 3 Bond angle restraints: 29970 Sorted by residual: angle pdb=" N SER B 150 " pdb=" CA SER B 150 " pdb=" C SER B 150 " ideal model delta sigma weight residual 113.61 96.80 16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb=" N TRP H 239 " pdb=" CA TRP H 239 " pdb=" C TRP H 239 " ideal model delta sigma weight residual 112.92 99.43 13.49 1.23e+00 6.61e-01 1.20e+02 angle pdb=" N LYS B 116 " pdb=" CA LYS B 116 " pdb=" C LYS B 116 " ideal model delta sigma weight residual 113.02 99.94 13.08 1.20e+00 6.94e-01 1.19e+02 angle pdb=" O3' A P 36 " pdb=" C3' A P 36 " pdb=" C2' A P 36 " ideal model delta sigma weight residual 109.50 122.55 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" N PRO D 54 " pdb=" CA PRO D 54 " pdb=" CB PRO D 54 " ideal model delta sigma weight residual 101.88 110.32 -8.44 1.01e+00 9.80e-01 6.99e+01 ... (remaining 29965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 11727 34.35 - 68.69: 938 68.69 - 103.04: 68 103.04 - 137.38: 3 137.38 - 171.73: 9 Dihedral angle restraints: 12745 sinusoidal: 5899 harmonic: 6846 Sorted by residual: dihedral pdb=" C MET B 156 " pdb=" N MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual -122.60 -154.82 32.22 0 2.50e+00 1.60e-01 1.66e+02 dihedral pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual 122.80 152.44 -29.64 0 2.50e+00 1.60e-01 1.41e+02 dihedral pdb=" O4' C P 44 " pdb=" C1' C P 44 " pdb=" N1 C P 44 " pdb=" C2 C P 44 " ideal model delta sinusoidal sigma weight residual 200.00 38.95 161.05 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 12742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3453 0.282 - 0.564: 16 0.564 - 0.847: 4 0.847 - 1.129: 0 1.129 - 1.411: 1 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CA MET B 156 " pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CB MET B 156 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" C3' DA Q 52 " pdb=" C4' DA Q 52 " pdb=" O3' DA Q 52 " pdb=" C2' DA Q 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.02 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CB VAL C 183 " pdb=" CA VAL C 183 " pdb=" CG1 VAL C 183 " pdb=" CG2 VAL C 183 " both_signs ideal model delta sigma weight residual False -2.63 -1.95 -0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3471 not shown) Planarity restraints: 3433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.095 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 157 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 154 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C ALA B 154 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA B 154 " 0.029 2.00e-02 2.50e+03 pdb=" N MET B 155 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 196 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C LYS B 196 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS B 196 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 197 " -0.022 2.00e-02 2.50e+03 ... (remaining 3430 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 25 1.89 - 2.65: 539 2.65 - 3.40: 27604 3.40 - 4.15: 58262 4.15 - 4.90: 98954 Nonbonded interactions: 185384 Sorted by model distance: nonbonded pdb=" ND2 ASN G 61 " pdb=" C5' DA Q 22 " model vdw 1.142 3.520 nonbonded pdb=" OD1 ASN B 222 " pdb=" OP1 DA R 37 " model vdw 1.181 3.040 nonbonded pdb=" C2 A P 31 " pdb=" C5 DC Q 20 " model vdw 1.244 3.640 nonbonded pdb=" N1 A P 31 " pdb=" N4 DC Q 20 " model vdw 1.246 3.200 nonbonded pdb=" N1 A P 31 " pdb=" C4 DC Q 20 " model vdw 1.355 3.340 ... (remaining 185379 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.340 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.007 0.108 21691 Z= 0.455 Angle : 1.132 16.808 29972 Z= 0.736 Chirality : 0.072 1.411 3474 Planarity : 0.007 0.142 3433 Dihedral : 22.140 171.731 8368 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.68 % Favored : 92.77 % Rotamer: Outliers : 2.60 % Allowed : 27.83 % Favored : 69.57 % Cbeta Deviations : 0.14 % 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: -3.09 (0.15), residues: 2379 helix: -2.54 (0.16), residues: 658 sheet: -0.82 (0.24), residues: 438 loop : -2.24 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 133 TYR 0.045 0.003 TYR H 81 PHE 0.044 0.002 PHE G 150 TRP 0.046 0.002 TRP H 28 HIS 0.020 0.002 HIS G 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.46 (21690) covalent geometry : angle 1.13138 / 0.74 (29970) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 2.55612 / 2.88 ( 2) hydrogen bonds : bond 0.24377 / 22.44 ( 638) hydrogen bonds : angle 9.60641 / 11.61 ( 1760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.7018 (mm) cc_final: 0.6737 (mm) REVERT: A 137 TYR cc_start: 0.8286 (m-10) cc_final: 0.8048 (m-10) REVERT: A 158 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7701 (mmmt) REVERT: A 159 MET cc_start: 0.8573 (mtp) cc_final: 0.8246 (mtp) REVERT: B 26 MET cc_start: 0.8717 (tpt) cc_final: 0.8185 (tpt) REVERT: B 108 ASP cc_start: 0.8457 (m-30) cc_final: 0.8249 (m-30) REVERT: B 146 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: B 152 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7229 (pttm) REVERT: B 155 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8273 (ptm) REVERT: B 172 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 197 HIS cc_start: 0.7781 (m170) cc_final: 0.7475 (m90) REVERT: B 214 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7764 (mtm) REVERT: C 38 MET cc_start: 0.7775 (mmm) cc_final: 0.7412 (mmp) REVERT: C 191 MET cc_start: 0.8220 (mtm) cc_final: 0.8009 (mtm) REVERT: C 224 MET cc_start: 0.8468 (mtp) cc_final: 0.8264 (mtp) REVERT: D 5 LYS cc_start: 0.7848 (mppt) cc_final: 0.7557 (mmtm) REVERT: D 217 ASP cc_start: 0.7005 (p0) cc_final: 0.6751 (p0) REVERT: E 204 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7388 (mt-10) REVERT: F 117 TYR cc_start: 0.6839 (t80) cc_final: 0.6221 (t80) REVERT: F 148 GLN cc_start: 0.7991 (pt0) cc_final: 0.7657 (pt0) REVERT: F 172 MET cc_start: 0.8561 (mtt) cc_final: 0.8361 (mtt) REVERT: G 63 GLN cc_start: 0.5462 (pm20) cc_final: 0.5076 (pm20) REVERT: G 200 PHE cc_start: 0.7796 (m-80) cc_final: 0.7537 (m-80) REVERT: H 156 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.6540 (tt) outliers start: 51 outliers final: 10 residues processed: 423 average time/residue: 0.1312 time to fit residues: 88.1547 Evaluate side-chains 280 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 63 GLN D 227 GLN E 33 ASN E 61 ASN E 63 GLN E 146 ASN F 61 ASN H 75 ASN H 189 HIS H 214 GLN I 47 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117883 restraints weight = 29731.349| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.95 r_work: 0.3192 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21691 Z= 0.209 Angle : 0.693 9.842 29972 Z= 0.393 Chirality : 0.049 0.372 3474 Planarity : 0.006 0.131 3433 Dihedral : 21.686 179.796 4265 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Rotamer: Outliers : 3.72 % Allowed : 24.62 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.72 (0.15), residues: 2379 helix: -2.01 (0.17), residues: 683 sheet: -0.88 (0.24), residues: 470 loop : -2.04 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 133 TYR 0.024 0.002 TYR H 117 PHE 0.021 0.001 PHE B 64 TRP 0.011 0.001 TRP F 239 HIS 0.006 0.001 HIS F 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (21690) covalent geometry : angle 0.69250 / 0.39 (29970) SS BOND : bond 0.00265 / 0.13 ( 1) SS BOND : angle 2.31468 / 3.34 ( 2) hydrogen bonds : bond 0.05470 / 5.16 ( 638) hydrogen bonds : angle 6.42691 / 7.83 ( 1760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 281 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8089 (mmmt) REVERT: A 159 MET cc_start: 0.8739 (mtp) cc_final: 0.8373 (mtp) REVERT: B 26 MET cc_start: 0.9077 (tpt) cc_final: 0.8728 (tpt) REVERT: B 108 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: B 115 ASP cc_start: 0.8679 (m-30) cc_final: 0.8235 (p0) REVERT: B 202 PHE cc_start: 0.8438 (p90) cc_final: 0.8177 (p90) REVERT: B 212 TYR cc_start: 0.9168 (m-80) cc_final: 0.8908 (m-80) REVERT: C 191 MET cc_start: 0.8778 (mtm) cc_final: 0.8562 (mtm) REVERT: C 275 ASP cc_start: 0.8093 (m-30) cc_final: 0.7250 (m-30) REVERT: D 5 LYS cc_start: 0.8068 (mppt) cc_final: 0.7689 (mmtm) REVERT: D 217 ASP cc_start: 0.7953 (p0) cc_final: 0.7687 (p0) REVERT: E 204 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7947 (mt-10) REVERT: E 245 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (t) REVERT: E 289 MET cc_start: 0.8859 (mtm) cc_final: 0.8651 (mtp) REVERT: F 33 ASN cc_start: 0.8043 (p0) cc_final: 0.7761 (p0) REVERT: G 262 TYR cc_start: 0.8839 (m-80) cc_final: 0.8242 (m-80) REVERT: H 159 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8014 (pp20) REVERT: I 135 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.5867 (p) outliers start: 73 outliers final: 33 residues processed: 333 average time/residue: 0.1293 time to fit residues: 68.4965 Evaluate side-chains 283 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 239 TRP Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 198 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 109 ASN D 146 ASN E 17 ASN E 61 ASN F 146 ASN F 148 GLN G 258 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107963 restraints weight = 29446.270| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.88 r_work: 0.3053 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21691 Z= 0.338 Angle : 0.734 10.306 29972 Z= 0.408 Chirality : 0.051 0.364 3474 Planarity : 0.006 0.133 3433 Dihedral : 21.551 178.249 4242 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.61 % Rotamer: Outliers : 4.54 % Allowed : 24.67 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.40 (0.16), residues: 2379 helix: -1.39 (0.18), residues: 637 sheet: -0.93 (0.25), residues: 425 loop : -1.95 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 22 TYR 0.018 0.002 TYR A 73 PHE 0.021 0.002 PHE B 64 TRP 0.015 0.002 TRP F 239 HIS 0.008 0.002 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.34 (21690) covalent geometry : angle 0.73375 / 0.41 (29970) SS BOND : bond 0.00272 / 0.14 ( 1) SS BOND : angle 2.25960 / 2.86 ( 2) hydrogen bonds : bond 0.05038 / 4.80 ( 638) hydrogen bonds : angle 5.91951 / 7.23 ( 1760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 232 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7836 (mp0) cc_final: 0.7544 (mp0) REVERT: A 97 ASP cc_start: 0.8041 (t0) cc_final: 0.7792 (t0) REVERT: A 158 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8262 (mmmt) REVERT: B 26 MET cc_start: 0.9204 (tpt) cc_final: 0.8814 (tpt) REVERT: B 62 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 115 ASP cc_start: 0.8713 (m-30) cc_final: 0.7866 (t0) REVERT: C 5 LYS cc_start: 0.6219 (tmtt) cc_final: 0.5887 (tmtt) REVERT: C 121 TYR cc_start: 0.9036 (t80) cc_final: 0.8231 (t80) REVERT: C 191 MET cc_start: 0.8788 (mtm) cc_final: 0.8528 (mtm) REVERT: D 5 LYS cc_start: 0.8239 (mppt) cc_final: 0.7830 (mmtm) REVERT: E 204 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8040 (mt-10) REVERT: E 289 MET cc_start: 0.8959 (mtm) cc_final: 0.8743 (mtp) REVERT: F 9 VAL cc_start: 0.8685 (t) cc_final: 0.8451 (p) REVERT: F 33 ASN cc_start: 0.8260 (p0) cc_final: 0.7971 (p0) REVERT: F 99 TYR cc_start: 0.9017 (t80) cc_final: 0.8709 (t80) REVERT: F 148 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: G 262 TYR cc_start: 0.9016 (m-80) cc_final: 0.8536 (m-80) REVERT: G 289 MET cc_start: 0.9102 (ttt) cc_final: 0.8771 (ttt) outliers start: 89 outliers final: 55 residues processed: 299 average time/residue: 0.1248 time to fit residues: 60.0734 Evaluate side-chains 270 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 127 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 247 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 138 ASN B 16 ASN B 180 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN F 146 ASN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.158095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113142 restraints weight = 29355.232| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.89 r_work: 0.3140 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21691 Z= 0.147 Angle : 0.600 9.431 29972 Z= 0.338 Chirality : 0.045 0.365 3474 Planarity : 0.005 0.134 3433 Dihedral : 21.450 178.987 4236 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.62 % Rotamer: Outliers : 3.52 % Allowed : 25.89 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.13 (0.16), residues: 2379 helix: -1.10 (0.19), residues: 652 sheet: -0.93 (0.24), residues: 454 loop : -1.76 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 263 TYR 0.019 0.001 TYR C 252 PHE 0.012 0.001 PHE B 32 TRP 0.010 0.001 TRP F 239 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (21690) covalent geometry : angle 0.60007 / 0.34 (29970) SS BOND : bond 0.00292 / 0.15 ( 1) SS BOND : angle 1.68018 / 2.75 ( 2) hydrogen bonds : bond 0.04236 / 3.98 ( 638) hydrogen bonds : angle 5.46846 / 6.73 ( 1760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7975 (mp0) cc_final: 0.7747 (mp0) REVERT: A 71 MET cc_start: 0.7726 (tpp) cc_final: 0.7525 (tpp) REVERT: A 115 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 150 GLN cc_start: 0.9027 (pm20) cc_final: 0.8772 (pm20) REVERT: B 26 MET cc_start: 0.9179 (tpt) cc_final: 0.8763 (tpt) REVERT: B 62 SER cc_start: 0.8755 (t) cc_final: 0.8435 (p) REVERT: B 108 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: B 115 ASP cc_start: 0.8590 (m-30) cc_final: 0.7801 (t0) REVERT: B 182 MET cc_start: 0.8800 (ttp) cc_final: 0.8216 (ttp) REVERT: C 5 LYS cc_start: 0.6436 (tmtt) cc_final: 0.6037 (tmtt) REVERT: C 121 TYR cc_start: 0.8975 (t80) cc_final: 0.8131 (t80) REVERT: C 275 ASP cc_start: 0.8067 (m-30) cc_final: 0.7722 (m-30) REVERT: D 5 LYS cc_start: 0.8167 (mppt) cc_final: 0.7823 (mmtm) REVERT: F 9 VAL cc_start: 0.8442 (t) cc_final: 0.8208 (p) REVERT: F 33 ASN cc_start: 0.8303 (p0) cc_final: 0.7959 (p0) REVERT: F 99 TYR cc_start: 0.8928 (t80) cc_final: 0.8563 (t80) REVERT: F 146 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (p0) REVERT: G 139 ILE cc_start: 0.7538 (mm) cc_final: 0.7320 (mm) REVERT: G 235 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8114 (p) REVERT: G 262 TYR cc_start: 0.8941 (m-80) cc_final: 0.8552 (m-80) REVERT: H 88 ASP cc_start: 0.7513 (t0) cc_final: 0.7271 (t0) REVERT: H 159 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: H 224 MET cc_start: 0.8257 (tpt) cc_final: 0.7985 (tpp) REVERT: H 263 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7523 (mtt-85) outliers start: 69 outliers final: 39 residues processed: 300 average time/residue: 0.1166 time to fit residues: 56.7609 Evaluate side-chains 276 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 239 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 247 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 146 ASN D 158 ASN F 146 ASN F 148 GLN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN G 294 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.154819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109921 restraints weight = 29148.588| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.83 r_work: 0.3087 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21691 Z= 0.235 Angle : 0.626 9.661 29972 Z= 0.348 Chirality : 0.047 0.361 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.426 178.310 4230 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.80 % Favored : 93.99 % Rotamer: Outliers : 4.13 % Allowed : 25.69 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.99 (0.16), residues: 2379 helix: -0.90 (0.19), residues: 646 sheet: -0.88 (0.24), residues: 454 loop : -1.71 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.020 0.002 TYR C 252 PHE 0.015 0.001 PHE D 200 TRP 0.009 0.001 TRP F 239 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (21690) covalent geometry : angle 0.62606 / 0.35 (29970) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 1.64283 / 2.44 ( 2) hydrogen bonds : bond 0.04286 / 4.05 ( 638) hydrogen bonds : angle 5.38835 / 6.58 ( 1760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 232 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8082 (mp0) cc_final: 0.7856 (mp0) REVERT: A 71 MET cc_start: 0.7790 (tpp) cc_final: 0.7581 (tpp) REVERT: B 26 MET cc_start: 0.9229 (tpt) cc_final: 0.8746 (tpt) REVERT: B 62 SER cc_start: 0.8845 (t) cc_final: 0.8406 (p) REVERT: B 108 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: B 115 ASP cc_start: 0.8483 (m-30) cc_final: 0.7817 (t0) REVERT: B 182 MET cc_start: 0.8859 (ttp) cc_final: 0.8254 (ttp) REVERT: C 5 LYS cc_start: 0.6425 (tmtt) cc_final: 0.6014 (tmtt) REVERT: C 121 TYR cc_start: 0.9041 (t80) cc_final: 0.8220 (t80) REVERT: D 5 LYS cc_start: 0.8189 (mppt) cc_final: 0.7817 (mmtm) REVERT: D 131 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8337 (ttt90) REVERT: D 133 ARG cc_start: 0.8889 (mtp85) cc_final: 0.8650 (mtp85) REVERT: D 227 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: F 9 VAL cc_start: 0.8539 (t) cc_final: 0.8291 (p) REVERT: F 33 ASN cc_start: 0.8407 (p0) cc_final: 0.8082 (p0) REVERT: F 99 TYR cc_start: 0.8982 (t80) cc_final: 0.8618 (t80) REVERT: F 148 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: F 162 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7411 (mp0) REVERT: G 235 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8116 (p) REVERT: G 262 TYR cc_start: 0.8994 (m-80) cc_final: 0.8688 (m-80) REVERT: H 88 ASP cc_start: 0.7467 (t0) cc_final: 0.7195 (t0) REVERT: H 118 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7067 (ttm170) REVERT: H 127 ARG cc_start: 0.6940 (ttm110) cc_final: 0.6693 (ttm110) REVERT: H 224 MET cc_start: 0.8358 (tpt) cc_final: 0.8098 (tpp) outliers start: 81 outliers final: 55 residues processed: 291 average time/residue: 0.1338 time to fit residues: 61.9731 Evaluate side-chains 285 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 204 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN C 146 ASN D 63 GLN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 ASN F 148 GLN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108660 restraints weight = 29038.972| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.83 r_work: 0.3079 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21691 Z= 0.239 Angle : 0.623 9.818 29972 Z= 0.346 Chirality : 0.046 0.362 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.411 178.467 4229 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.84 % Favored : 93.95 % Rotamer: Outliers : 4.49 % Allowed : 25.48 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.91 (0.16), residues: 2379 helix: -0.81 (0.19), residues: 643 sheet: -0.85 (0.25), residues: 441 loop : -1.66 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 133 TYR 0.020 0.002 TYR C 252 PHE 0.024 0.001 PHE B 202 TRP 0.008 0.001 TRP F 239 HIS 0.007 0.002 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (21690) covalent geometry : angle 0.62280 / 0.35 (29970) SS BOND : bond 0.00124 / 0.06 ( 1) SS BOND : angle 3.61800 / 5.26 ( 2) hydrogen bonds : bond 0.04230 / 4.00 ( 638) hydrogen bonds : angle 5.33319 / 6.52 ( 1760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 233 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7860 (tpp) cc_final: 0.7629 (tpp) REVERT: A 97 ASP cc_start: 0.7969 (t0) cc_final: 0.7616 (t0) REVERT: B 26 MET cc_start: 0.9236 (tpt) cc_final: 0.8783 (tpt) REVERT: B 62 SER cc_start: 0.8795 (t) cc_final: 0.8441 (p) REVERT: B 108 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: B 115 ASP cc_start: 0.8480 (m-30) cc_final: 0.7843 (t0) REVERT: B 182 MET cc_start: 0.8858 (ttp) cc_final: 0.8230 (ttp) REVERT: C 5 LYS cc_start: 0.6479 (tmtt) cc_final: 0.5969 (tmtt) REVERT: C 121 TYR cc_start: 0.9030 (t80) cc_final: 0.8213 (t80) REVERT: D 5 LYS cc_start: 0.8173 (mppt) cc_final: 0.7801 (mmtm) REVERT: D 131 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8356 (ttt90) REVERT: D 227 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: F 9 VAL cc_start: 0.8590 (t) cc_final: 0.8346 (p) REVERT: F 33 ASN cc_start: 0.8379 (p0) cc_final: 0.8027 (p0) REVERT: F 148 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: F 162 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7462 (mp0) REVERT: G 235 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8122 (p) REVERT: G 262 TYR cc_start: 0.8992 (m-80) cc_final: 0.8775 (m-80) REVERT: H 88 ASP cc_start: 0.7452 (t0) cc_final: 0.7159 (t0) REVERT: H 118 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7186 (ttm170) REVERT: H 159 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: H 224 MET cc_start: 0.8324 (tpt) cc_final: 0.8078 (tpp) outliers start: 88 outliers final: 61 residues processed: 294 average time/residue: 0.1335 time to fit residues: 62.3708 Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 84 optimal weight: 0.7980 chunk 247 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN D 63 GLN D 72 HIS D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112171 restraints weight = 29145.783| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21691 Z= 0.147 Angle : 0.587 9.311 29972 Z= 0.326 Chirality : 0.044 0.363 3474 Planarity : 0.005 0.134 3433 Dihedral : 21.383 178.901 4229 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.55 % Favored : 94.24 % Rotamer: Outliers : 3.41 % Allowed : 26.50 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.79 (0.16), residues: 2379 helix: -0.67 (0.19), residues: 643 sheet: -0.83 (0.25), residues: 445 loop : -1.59 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.014 0.001 TYR D 190 PHE 0.014 0.001 PHE I 41 TRP 0.023 0.001 TRP H 239 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (21690) covalent geometry : angle 0.58609 / 0.33 (29970) SS BOND : bond 0.00266 / 0.13 ( 1) SS BOND : angle 2.93608 / 4.35 ( 2) hydrogen bonds : bond 0.03933 / 3.73 ( 638) hydrogen bonds : angle 5.20605 / 6.39 ( 1760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8077 (t0) cc_final: 0.7722 (t0) REVERT: B 26 MET cc_start: 0.9165 (tpt) cc_final: 0.8727 (tpt) REVERT: B 62 SER cc_start: 0.8809 (t) cc_final: 0.8473 (p) REVERT: B 108 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: B 115 ASP cc_start: 0.8500 (m-30) cc_final: 0.7897 (t0) REVERT: B 182 MET cc_start: 0.8881 (ttp) cc_final: 0.8246 (ttp) REVERT: C 5 LYS cc_start: 0.6568 (tmtt) cc_final: 0.6023 (tmtt) REVERT: C 121 TYR cc_start: 0.9005 (t80) cc_final: 0.8138 (t80) REVERT: C 183 VAL cc_start: 0.8991 (m) cc_final: 0.8673 (p) REVERT: D 5 LYS cc_start: 0.8135 (mppt) cc_final: 0.7780 (mmtm) REVERT: D 38 MET cc_start: 0.8991 (mmt) cc_final: 0.8632 (mmp) REVERT: D 131 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8278 (ttt90) REVERT: D 185 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8617 (mt) REVERT: E 202 SER cc_start: 0.9129 (p) cc_final: 0.8910 (p) REVERT: F 9 VAL cc_start: 0.8461 (t) cc_final: 0.8209 (p) REVERT: F 33 ASN cc_start: 0.8384 (p0) cc_final: 0.8041 (p0) REVERT: F 162 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7498 (mp0) REVERT: G 235 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8150 (p) REVERT: G 262 TYR cc_start: 0.8981 (m-80) cc_final: 0.8742 (m-80) REVERT: H 38 MET cc_start: 0.7757 (mmm) cc_final: 0.7147 (mmm) REVERT: H 88 ASP cc_start: 0.7415 (t0) cc_final: 0.7112 (t0) REVERT: H 118 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7244 (ttm170) REVERT: H 159 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: H 224 MET cc_start: 0.8382 (tpt) cc_final: 0.8162 (tpp) outliers start: 67 outliers final: 48 residues processed: 283 average time/residue: 0.1222 time to fit residues: 55.0334 Evaluate side-chains 279 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 139 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 4 optimal weight: 50.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN D 63 GLN D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109833 restraints weight = 28955.398| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.91 r_work: 0.3063 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21691 Z= 0.218 Angle : 0.616 9.554 29972 Z= 0.340 Chirality : 0.046 0.361 3474 Planarity : 0.005 0.136 3433 Dihedral : 21.377 178.726 4229 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 3.82 % Allowed : 26.30 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.76 (0.16), residues: 2379 helix: -0.62 (0.19), residues: 643 sheet: -0.77 (0.25), residues: 435 loop : -1.60 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.014 0.002 TYR H 117 PHE 0.017 0.001 PHE H 160 TRP 0.026 0.001 TRP H 239 HIS 0.007 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (21690) covalent geometry : angle 0.61515 / 0.34 (29970) SS BOND : bond 0.00335 / 0.17 ( 1) SS BOND : angle 3.03522 / 4.33 ( 2) hydrogen bonds : bond 0.04014 / 3.82 ( 638) hydrogen bonds : angle 5.21930 / 6.41 ( 1760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9144 (tp) cc_final: 0.8766 (tp) REVERT: A 97 ASP cc_start: 0.8107 (t0) cc_final: 0.7698 (t0) REVERT: A 115 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 26 MET cc_start: 0.9248 (tpt) cc_final: 0.8792 (tpt) REVERT: B 52 TYR cc_start: 0.8997 (p90) cc_final: 0.8794 (p90) REVERT: B 62 SER cc_start: 0.8819 (t) cc_final: 0.8490 (p) REVERT: B 108 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: B 115 ASP cc_start: 0.8545 (m-30) cc_final: 0.7952 (t0) REVERT: B 182 MET cc_start: 0.8914 (ttp) cc_final: 0.8278 (ttp) REVERT: C 5 LYS cc_start: 0.6617 (tmtt) cc_final: 0.6037 (tmtt) REVERT: C 121 TYR cc_start: 0.9030 (t80) cc_final: 0.8209 (t80) REVERT: C 183 VAL cc_start: 0.9033 (m) cc_final: 0.8709 (p) REVERT: D 5 LYS cc_start: 0.8196 (mppt) cc_final: 0.7836 (mmtm) REVERT: D 131 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8378 (ttt90) REVERT: D 227 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: E 117 TYR cc_start: 0.8974 (t80) cc_final: 0.8762 (t80) REVERT: F 9 VAL cc_start: 0.8553 (t) cc_final: 0.8300 (p) REVERT: F 33 ASN cc_start: 0.8399 (p0) cc_final: 0.8056 (p0) REVERT: F 162 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7503 (mp0) REVERT: G 235 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (p) REVERT: H 38 MET cc_start: 0.7767 (mmm) cc_final: 0.7153 (mmm) REVERT: H 88 ASP cc_start: 0.7438 (t0) cc_final: 0.7126 (t0) REVERT: H 118 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7315 (ttm170) REVERT: H 224 MET cc_start: 0.8351 (tpt) cc_final: 0.8127 (tpp) outliers start: 75 outliers final: 63 residues processed: 278 average time/residue: 0.1228 time to fit residues: 54.9963 Evaluate side-chains 285 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 0.0030 chunk 218 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 chunk 151 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN B 222 ASN C 146 ASN D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114701 restraints weight = 29001.886| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.79 r_work: 0.3150 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21691 Z= 0.135 Angle : 0.582 9.228 29972 Z= 0.322 Chirality : 0.044 0.361 3474 Planarity : 0.005 0.136 3433 Dihedral : 21.348 179.376 4229 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 3.36 % Allowed : 27.17 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.58 (0.17), residues: 2379 helix: -0.47 (0.20), residues: 643 sheet: -0.57 (0.26), residues: 395 loop : -1.50 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.020 0.001 TYR H 81 PHE 0.010 0.001 PHE B 32 TRP 0.041 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (21690) covalent geometry : angle 0.58129 / 0.32 (29970) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 2.85314 / 4.31 ( 2) hydrogen bonds : bond 0.03738 / 3.55 ( 638) hydrogen bonds : angle 5.04571 / 6.22 ( 1760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9165 (tp) cc_final: 0.8825 (tp) REVERT: A 97 ASP cc_start: 0.8004 (t0) cc_final: 0.7711 (t0) REVERT: B 26 MET cc_start: 0.9121 (tpt) cc_final: 0.8734 (tpt) REVERT: B 108 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: B 115 ASP cc_start: 0.8373 (m-30) cc_final: 0.7927 (t0) REVERT: B 182 MET cc_start: 0.8783 (ttp) cc_final: 0.8266 (ttp) REVERT: B 214 MET cc_start: 0.8436 (mmm) cc_final: 0.8233 (mmm) REVERT: C 5 LYS cc_start: 0.6651 (tmtt) cc_final: 0.6036 (tmtt) REVERT: C 121 TYR cc_start: 0.8919 (t80) cc_final: 0.8101 (t80) REVERT: C 183 VAL cc_start: 0.8872 (m) cc_final: 0.8598 (p) REVERT: D 5 LYS cc_start: 0.8124 (mppt) cc_final: 0.7864 (mmtm) REVERT: D 131 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7748 (tpt90) REVERT: D 185 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8516 (mt) REVERT: D 227 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: E 117 TYR cc_start: 0.8731 (t80) cc_final: 0.8522 (t80) REVERT: E 202 SER cc_start: 0.9051 (p) cc_final: 0.8831 (p) REVERT: F 9 VAL cc_start: 0.8343 (t) cc_final: 0.8100 (p) REVERT: F 33 ASN cc_start: 0.8354 (p0) cc_final: 0.8005 (p0) REVERT: F 162 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7427 (mp0) REVERT: G 235 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8161 (p) REVERT: H 38 MET cc_start: 0.7765 (mmm) cc_final: 0.7144 (mmm) REVERT: H 78 LEU cc_start: 0.7661 (tp) cc_final: 0.7440 (tp) REVERT: H 88 ASP cc_start: 0.7313 (t0) cc_final: 0.7033 (t0) REVERT: H 119 TYR cc_start: 0.7798 (m-10) cc_final: 0.7568 (m-10) REVERT: H 263 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7209 (mtt-85) outliers start: 66 outliers final: 52 residues processed: 289 average time/residue: 0.1268 time to fit residues: 59.7887 Evaluate side-chains 289 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 202 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 chunk 98 optimal weight: 0.0010 chunk 18 optimal weight: 0.8980 chunk 167 optimal weight: 0.0270 chunk 55 optimal weight: 0.0370 chunk 140 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 180 GLN C 146 ASN D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115966 restraints weight = 29147.336| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.69 r_work: 0.3186 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21691 Z= 0.128 Angle : 0.585 9.001 29972 Z= 0.322 Chirality : 0.043 0.359 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.303 179.497 4229 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 3.11 % Allowed : 27.37 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.47 (0.17), residues: 2379 helix: -0.37 (0.20), residues: 646 sheet: -0.51 (0.27), residues: 395 loop : -1.44 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 133 TYR 0.034 0.001 TYR B 217 PHE 0.029 0.001 PHE B 202 TRP 0.045 0.001 TRP H 239 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (21690) covalent geometry : angle 0.58293 / 0.32 (29970) SS BOND : bond 0.04526 / 2.26 ( 1) SS BOND : angle 5.46939 / 11.24 ( 2) hydrogen bonds : bond 0.04050 / 3.55 ( 638) hydrogen bonds : angle 4.96795 / 6.14 ( 1760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8972 (p90) cc_final: 0.8717 (p90) REVERT: A 32 ILE cc_start: 0.9102 (tp) cc_final: 0.8793 (tp) REVERT: A 97 ASP cc_start: 0.7986 (t0) cc_final: 0.7691 (t0) REVERT: B 26 MET cc_start: 0.9105 (tpt) cc_final: 0.8790 (tpt) REVERT: B 108 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8161 (m-30) REVERT: B 115 ASP cc_start: 0.8283 (m-30) cc_final: 0.7895 (t0) REVERT: B 182 MET cc_start: 0.8720 (ttp) cc_final: 0.8219 (ttp) REVERT: B 198 MET cc_start: 0.8462 (mmm) cc_final: 0.8257 (tpt) REVERT: C 5 LYS cc_start: 0.6585 (tttt) cc_final: 0.6006 (tmtt) REVERT: C 121 TYR cc_start: 0.8910 (t80) cc_final: 0.8139 (t80) REVERT: C 183 VAL cc_start: 0.8740 (m) cc_final: 0.8478 (p) REVERT: C 301 PHE cc_start: 0.8076 (m-10) cc_final: 0.7852 (m-10) REVERT: D 5 LYS cc_start: 0.8107 (mppt) cc_final: 0.7857 (mmtm) REVERT: D 38 MET cc_start: 0.8683 (mmp) cc_final: 0.8441 (mmp) REVERT: D 227 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: E 202 SER cc_start: 0.9019 (p) cc_final: 0.8788 (p) REVERT: F 33 ASN cc_start: 0.8349 (p0) cc_final: 0.7993 (p0) REVERT: F 162 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7436 (mp0) REVERT: G 235 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8139 (p) REVERT: H 38 MET cc_start: 0.7722 (mmm) cc_final: 0.7091 (mmm) REVERT: H 78 LEU cc_start: 0.7660 (tp) cc_final: 0.7440 (tp) REVERT: H 88 ASP cc_start: 0.7267 (t0) cc_final: 0.7002 (t0) REVERT: H 169 ILE cc_start: 0.6998 (tt) cc_final: 0.6739 (tp) REVERT: H 263 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7256 (mtt-85) outliers start: 61 outliers final: 48 residues processed: 286 average time/residue: 0.1227 time to fit residues: 57.2796 Evaluate side-chains 289 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 55 optimal weight: 0.3980 chunk 196 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.157726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115158 restraints weight = 29144.872| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.80 r_work: 0.3150 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21691 Z= 0.162 Angle : 0.592 9.172 29972 Z= 0.325 Chirality : 0.044 0.357 3474 Planarity : 0.005 0.134 3433 Dihedral : 21.272 179.486 4229 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 2.85 % Allowed : 27.37 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.43 (0.17), residues: 2379 helix: -0.33 (0.20), residues: 647 sheet: -0.54 (0.26), residues: 405 loop : -1.41 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 133 TYR 0.028 0.001 TYR H 81 PHE 0.029 0.001 PHE B 202 TRP 0.038 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (21690) covalent geometry : angle 0.59058 / 0.32 (29970) SS BOND : bond 0.00935 / 0.47 ( 1) SS BOND : angle 4.99965 / 9.19 ( 2) hydrogen bonds : bond 0.03981 / 3.54 ( 638) hydrogen bonds : angle 4.96128 / 6.12 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5649.25 seconds wall clock time: 97 minutes 33.47 seconds (5853.47 seconds total)