Starting phenix.real_space_refine on Fri Aug 7 09:19:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k29_36835/08_2026/8k29_36835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k29_36835/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k29_36835/08_2026/8k29_36835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k29_36835/08_2026/8k29_36835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k29_36835/08_2026/8k29_36835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k29_36835/08_2026/8k29_36835.map" } 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-2.2rc3-6140/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: 3.99, per 1000 atoms: 0.19 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 927.9 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: 2.76 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: 3.87 Time building geometry restraints manager: 2.25 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: 29371 3.36 - 6.72: 506 6.72 - 10.09: 79 10.09 - 13.45: 9 13.45 - 16.81: 5 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=" 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 angle pdb=" N LYS A 3 " pdb=" CA LYS A 3 " pdb=" C LYS A 3 " ideal model delta sigma weight residual 113.55 103.63 9.92 1.26e+00 6.30e-01 6.20e+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: 3454 0.282 - 0.564: 15 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: 1.000 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 21.510 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- 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= 0.462 Angle : 1.144 16.808 29972 Z= 0.750 Chirality : 0.073 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 1.14349 / 0.75 (29970) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 2.55612 / 2.88 ( 2) hydrogen bonds : bond 0.24377 / 25.11 ( 638) hydrogen bonds : angle 9.60641 / 12.08 ( 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 : 0.603 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: 0.6736 (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: 0.7760 (mmmt) REVERT: A 159 MET cc_start: 0.8573 (mtp) cc_final: 0.8245 (mtp) REVERT: B 26 MET cc_start: 0.8717 (tpt) cc_final: 0.8186 (tpt) REVERT: B 108 ASP cc_start: 0.8457 (m-30) cc_final: 0.8250 (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: 0.7228 (pttm) REVERT: B 155 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (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 199 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8142 (mtp180) REVERT: B 214 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7763 (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: G 63 GLN cc_start: 0.5462 (pm20) cc_final: 0.5071 (pm20) REVERT: G 200 PHE cc_start: 0.7796 (m-80) cc_final: 0.7538 (m-80) REVERT: H 156 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.6539 (tt) outliers start: 51 outliers final: 10 residues processed: 423 average time/residue: 0.1419 time to fit residues: 95.0114 Evaluate side-chains 284 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 199 ARG 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 227 GLN E 33 ASN E 61 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 61 ASN F 63 GLN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN H 189 HIS H 214 GLN I 47 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117753 restraints weight = 29727.996| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.96 r_work: 0.3190 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 0.057 21691 Z= 0.208 Angle : 0.705 10.368 29972 Z= 0.394 Chirality : 0.050 0.492 3474 Planarity : 0.006 0.133 3433 Dihedral : 21.680 175.165 4269 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.84 % Favored : 93.86 % Rotamer: Outliers : 3.87 % Allowed : 24.97 % Favored : 71.15 % 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 0.005 0.001 ARG H 118 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 0.00430 / 0.21 (21690) covalent geometry : angle 0.70464 / 0.39 (29970) SS BOND : bond 0.00277 / 0.14 ( 1) SS BOND : angle 2.23188 / 3.24 ( 2) hydrogen bonds : bond 0.05439 / 5.68 ( 638) hydrogen bonds : angle 6.41915 / 8.11 ( 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 360 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 284 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7686 (t0) cc_final: 0.7133 (t0) REVERT: A 159 MET cc_start: 0.8745 (mtp) cc_final: 0.8382 (mtp) REVERT: B 26 MET cc_start: 0.9080 (tpt) cc_final: 0.8733 (tpt) REVERT: B 108 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 115 ASP cc_start: 0.8685 (m-30) cc_final: 0.8254 (p0) REVERT: B 202 PHE cc_start: 0.8435 (p90) cc_final: 0.8184 (p90) REVERT: B 212 TYR cc_start: 0.9176 (m-80) cc_final: 0.8920 (m-80) REVERT: C 121 TYR cc_start: 0.9014 (t80) cc_final: 0.8224 (t80) REVERT: C 191 MET cc_start: 0.8783 (mtm) cc_final: 0.8569 (mtm) REVERT: C 275 ASP cc_start: 0.8099 (m-30) cc_final: 0.7258 (m-30) REVERT: D 5 LYS cc_start: 0.8065 (mppt) cc_final: 0.7687 (mmtm) REVERT: D 217 ASP cc_start: 0.7952 (p0) cc_final: 0.7686 (p0) REVERT: E 204 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: E 245 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7869 (t) REVERT: E 289 MET cc_start: 0.8853 (mtm) cc_final: 0.8646 (mtp) REVERT: F 33 ASN cc_start: 0.8031 (p0) cc_final: 0.7758 (p0) REVERT: G 262 TYR cc_start: 0.8840 (m-80) cc_final: 0.8239 (m-80) REVERT: H 159 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: I 135 VAL cc_start: 0.6349 (OUTLIER) cc_final: 0.5851 (p) outliers start: 76 outliers final: 34 residues processed: 336 average time/residue: 0.1364 time to fit residues: 72.5314 Evaluate side-chains 287 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 188 GLU 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 204 GLU 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: 6.9990 chunk 200 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 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: 0.7980 chunk 177 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 50.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN 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 F 146 ASN F 148 GLN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113169 restraints weight = 29498.824| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.96 r_work: 0.3114 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21691 Z= 0.222 Angle : 0.659 10.350 29972 Z= 0.366 Chirality : 0.049 0.466 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.489 174.022 4238 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 4.03 % Allowed : 24.36 % Favored : 71.61 % 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: -2.31 (0.16), residues: 2379 helix: -1.40 (0.18), residues: 652 sheet: -0.84 (0.25), residues: 449 loop : -1.87 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.017 0.002 TYR A 137 PHE 0.018 0.002 PHE B 64 TRP 0.013 0.001 TRP F 239 HIS 0.006 0.002 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (21690) covalent geometry : angle 0.65893 / 0.37 (29970) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 1.86631 / 2.47 ( 2) hydrogen bonds : bond 0.04645 / 4.81 ( 638) hydrogen bonds : angle 5.76471 / 7.35 ( 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 331 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 252 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 MET cc_start: 0.9119 (tpt) cc_final: 0.8778 (tpt) REVERT: B 62 SER cc_start: 0.8806 (t) cc_final: 0.8454 (p) REVERT: B 115 ASP cc_start: 0.8704 (m-30) cc_final: 0.7884 (t0) REVERT: C 5 LYS cc_start: 0.6168 (tmtt) cc_final: 0.5492 (tmtt) REVERT: C 121 TYR cc_start: 0.9000 (t80) cc_final: 0.8183 (t80) REVERT: C 191 MET cc_start: 0.8808 (mtm) cc_final: 0.8558 (mtm) REVERT: D 5 LYS cc_start: 0.8205 (mppt) cc_final: 0.7825 (mmtm) REVERT: D 200 PHE cc_start: 0.9143 (m-80) cc_final: 0.8937 (m-80) REVERT: E 204 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8016 (mt-10) REVERT: F 9 VAL cc_start: 0.8445 (t) cc_final: 0.8202 (p) REVERT: F 33 ASN cc_start: 0.8180 (p0) cc_final: 0.7828 (p0) REVERT: F 99 TYR cc_start: 0.8944 (t80) cc_final: 0.8582 (t80) REVERT: F 148 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: G 262 TYR cc_start: 0.8892 (m-80) cc_final: 0.8340 (m-80) REVERT: G 289 MET cc_start: 0.9036 (ttt) cc_final: 0.8716 (ttt) outliers start: 79 outliers final: 50 residues processed: 311 average time/residue: 0.1166 time to fit residues: 58.6849 Evaluate side-chains 280 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 152 CYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 114 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 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 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 204 GLU 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 206 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 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 148 GLN Chi-restraints excluded: chain F residue 172 MET 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 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 62 ILE Chi-restraints excluded: chain H residue 233 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 75 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 127 optimal weight: 0.0870 chunk 215 optimal weight: 10.0000 chunk 189 optimal weight: 0.0770 chunk 218 optimal weight: 8.9990 chunk 31 optimal weight: 0.1980 chunk 158 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN E 17 ASN E 61 ASN F 146 ASN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117247 restraints weight = 29487.607| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.94 r_work: 0.3174 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21691 Z= 0.131 Angle : 0.594 9.774 29972 Z= 0.330 Chirality : 0.046 0.450 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.407 174.432 4233 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 3.41 % Allowed : 25.23 % Favored : 71.36 % 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: -2.08 (0.16), residues: 2379 helix: -1.03 (0.19), residues: 650 sheet: -1.03 (0.23), residues: 485 loop : -1.70 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 14 TYR 0.018 0.001 TYR C 252 PHE 0.015 0.001 PHE G 150 TRP 0.013 0.001 TRP E 239 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (21690) covalent geometry : angle 0.59395 / 0.33 (29970) SS BOND : bond 0.00305 / 0.15 ( 1) SS BOND : angle 1.55015 / 2.57 ( 2) hydrogen bonds : bond 0.04131 / 4.22 ( 638) hydrogen bonds : angle 5.40892 / 6.90 ( 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 326 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7905 (t0) cc_final: 0.7366 (t0) REVERT: B 26 MET cc_start: 0.9110 (tpt) cc_final: 0.8779 (tpt) REVERT: B 62 SER cc_start: 0.8801 (t) cc_final: 0.8472 (p) REVERT: B 108 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: B 115 ASP cc_start: 0.8596 (m-30) cc_final: 0.7802 (t0) REVERT: B 182 MET cc_start: 0.8765 (ttp) cc_final: 0.8285 (ttp) REVERT: C 5 LYS cc_start: 0.6291 (tmtt) cc_final: 0.5946 (tmtt) REVERT: C 121 TYR cc_start: 0.8973 (t80) cc_final: 0.8165 (t80) REVERT: C 183 VAL cc_start: 0.8847 (m) cc_final: 0.8546 (p) REVERT: C 275 ASP cc_start: 0.8129 (m-30) cc_final: 0.7719 (m-30) REVERT: C 301 PHE cc_start: 0.7774 (m-10) cc_final: 0.7564 (m-10) REVERT: D 5 LYS cc_start: 0.8141 (mppt) cc_final: 0.7788 (mmtm) REVERT: D 38 MET cc_start: 0.8862 (mmt) cc_final: 0.8451 (mmt) REVERT: D 133 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8621 (mtp-110) REVERT: E 61 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (p0) REVERT: E 130 TRP cc_start: 0.8781 (m100) cc_final: 0.8572 (m100) REVERT: E 156 LEU cc_start: 0.8213 (mp) cc_final: 0.7983 (mt) REVERT: F 33 ASN cc_start: 0.8235 (p0) cc_final: 0.7903 (p0) REVERT: F 99 TYR cc_start: 0.8930 (t80) cc_final: 0.8646 (t80) REVERT: F 148 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: G 150 PHE cc_start: 0.8070 (m-80) cc_final: 0.7858 (m-10) REVERT: G 235 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8080 (p) REVERT: G 262 TYR cc_start: 0.8833 (m-80) cc_final: 0.8322 (m-80) REVERT: H 38 MET cc_start: 0.7708 (mmm) cc_final: 0.7150 (mmm) REVERT: H 191 MET cc_start: 0.6152 (pmm) cc_final: 0.5569 (pmm) REVERT: H 203 GLN cc_start: 0.7914 (mp10) cc_final: 0.7647 (mp10) REVERT: H 224 MET cc_start: 0.8250 (tpt) cc_final: 0.7983 (tpp) outliers start: 67 outliers final: 39 residues processed: 306 average time/residue: 0.1333 time to fit residues: 65.3672 Evaluate side-chains 287 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 108 ASP 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 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 C residue 188 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 274 MET 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 206 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 61 ASN 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 E residue 224 MET 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 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 H residue 233 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 247 optimal weight: 40.0000 chunk 56 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 146 ASN D 158 ASN E 61 ASN F 146 ASN F 148 GLN ** G 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 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 = 0.3895 r_free = 0.3895 target = 0.155097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112187 restraints weight = 29298.888| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.11 r_work: 0.3053 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 21691 Z= 0.275 Angle : 0.662 10.280 29972 Z= 0.361 Chirality : 0.049 0.436 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.370 173.636 4229 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 4.08 % Allowed : 25.79 % Favored : 70.13 % 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: -1.98 (0.16), residues: 2379 helix: -0.92 (0.19), residues: 647 sheet: -0.82 (0.24), residues: 442 loop : -1.71 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 22 TYR 0.021 0.002 TYR C 252 PHE 0.016 0.002 PHE D 200 TRP 0.009 0.002 TRP F 239 HIS 0.006 0.002 HIS G 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (21690) covalent geometry : angle 0.66152 / 0.36 (29970) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 3.38260 / 4.17 ( 2) hydrogen bonds : bond 0.04335 / 4.48 ( 638) hydrogen bonds : angle 5.40794 / 6.82 ( 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 320 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9076 (tp) cc_final: 0.8732 (tp) REVERT: A 150 GLN cc_start: 0.9182 (pm20) cc_final: 0.8831 (pm20) REVERT: B 26 MET cc_start: 0.9235 (tpt) cc_final: 0.8781 (tpt) REVERT: B 62 SER cc_start: 0.8880 (t) cc_final: 0.8562 (p) REVERT: B 108 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 115 ASP cc_start: 0.8548 (m-30) cc_final: 0.7856 (t0) REVERT: B 182 MET cc_start: 0.8878 (ttp) cc_final: 0.8270 (ttp) REVERT: C 5 LYS cc_start: 0.6440 (tmtt) cc_final: 0.6059 (tmtt) REVERT: C 121 TYR cc_start: 0.9031 (t80) cc_final: 0.8218 (t80) REVERT: C 183 VAL cc_start: 0.9097 (m) cc_final: 0.8807 (p) REVERT: D 5 LYS cc_start: 0.8198 (mppt) cc_final: 0.7816 (mmtm) REVERT: F 9 VAL cc_start: 0.8583 (t) cc_final: 0.8347 (p) REVERT: F 33 ASN cc_start: 0.8404 (p0) cc_final: 0.8078 (p0) REVERT: F 99 TYR cc_start: 0.8979 (t80) cc_final: 0.8724 (t80) REVERT: F 148 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: G 262 TYR cc_start: 0.9014 (m-80) cc_final: 0.8625 (m-80) REVERT: H 118 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7140 (ttm170) REVERT: H 127 ARG cc_start: 0.6945 (ttm110) cc_final: 0.6709 (ttm110) REVERT: H 224 MET cc_start: 0.8314 (tpt) cc_final: 0.8010 (tpp) outliers start: 80 outliers final: 57 residues processed: 296 average time/residue: 0.1221 time to fit residues: 58.6770 Evaluate side-chains 288 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 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 114 THR Chi-restraints excluded: chain D residue 183 VAL 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 151 THR 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 172 MET 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 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 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: 6.9990 chunk 210 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN 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 G 132 ASN ** G 227 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113859 restraints weight = 29091.872| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.89 r_work: 0.3120 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21691 Z= 0.164 Angle : 0.602 10.058 29972 Z= 0.331 Chirality : 0.046 0.430 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.337 174.566 4229 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.45 % Rotamer: Outliers : 4.18 % Allowed : 26.15 % Favored : 69.67 % 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: -1.84 (0.16), residues: 2379 helix: -0.71 (0.19), residues: 643 sheet: -0.85 (0.24), residues: 440 loop : -1.62 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 133 TYR 0.018 0.001 TYR C 252 PHE 0.025 0.001 PHE B 202 TRP 0.009 0.001 TRP F 239 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (21690) covalent geometry : angle 0.60192 / 0.33 (29970) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 2.85282 / 4.07 ( 2) hydrogen bonds : bond 0.04012 / 4.12 ( 638) hydrogen bonds : angle 5.23437 / 6.64 ( 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 335 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9104 (tp) cc_final: 0.8745 (tp) REVERT: B 26 MET cc_start: 0.9136 (tpt) cc_final: 0.8682 (tpt) REVERT: B 62 SER cc_start: 0.8847 (t) cc_final: 0.8441 (p) REVERT: B 108 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: B 115 ASP cc_start: 0.8487 (m-30) cc_final: 0.7911 (t0) REVERT: B 182 MET cc_start: 0.8869 (ttp) cc_final: 0.8273 (ttp) REVERT: C 5 LYS cc_start: 0.6519 (tmtt) cc_final: 0.6079 (tmtt) REVERT: C 121 TYR cc_start: 0.8947 (t80) cc_final: 0.8125 (t80) REVERT: C 183 VAL cc_start: 0.8953 (m) cc_final: 0.8686 (p) REVERT: D 5 LYS cc_start: 0.8131 (mppt) cc_final: 0.7824 (mmtm) REVERT: D 131 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8192 (ttt90) REVERT: D 227 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: F 9 VAL cc_start: 0.8420 (t) cc_final: 0.8197 (p) REVERT: F 33 ASN cc_start: 0.8362 (p0) cc_final: 0.8023 (p0) REVERT: F 99 TYR cc_start: 0.8915 (t80) cc_final: 0.8691 (t80) REVERT: F 148 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: G 235 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8084 (p) REVERT: G 262 TYR cc_start: 0.8927 (m-80) cc_final: 0.8612 (m-80) REVERT: H 38 MET cc_start: 0.7772 (mmm) cc_final: 0.7155 (mmm) REVERT: H 118 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7186 (ttm170) REVERT: H 127 ARG cc_start: 0.6956 (ttm110) cc_final: 0.6701 (ttm110) REVERT: H 224 MET cc_start: 0.8363 (tpt) cc_final: 0.8116 (tpp) outliers start: 82 outliers final: 54 residues processed: 311 average time/residue: 0.1380 time to fit residues: 69.3912 Evaluate side-chains 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 40 SER Chi-restraints excluded: chain B residue 101 CYS 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 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 188 GLU 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 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 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 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 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 G residue 273 LEU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 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 75 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 84 optimal weight: 0.8980 chunk 247 optimal weight: 40.0000 chunk 245 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 84 ASN D 63 GLN D 146 ASN D 158 ASN F 63 GLN F 146 ASN F 148 GLN ** G 227 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.157695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113617 restraints weight = 29095.426| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.79 r_work: 0.3153 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21691 Z= 0.147 Angle : 0.592 9.896 29972 Z= 0.327 Chirality : 0.045 0.425 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.324 174.486 4229 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.59 % Favored : 94.20 % Rotamer: Outliers : 3.52 % Allowed : 26.40 % 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: -1.73 (0.16), residues: 2379 helix: -0.58 (0.20), residues: 643 sheet: -0.89 (0.25), residues: 439 loop : -1.54 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 133 TYR 0.013 0.001 TYR H 117 PHE 0.028 0.001 PHE B 202 TRP 0.009 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (21690) covalent geometry : angle 0.59198 / 0.33 (29970) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 2.67470 / 3.77 ( 2) hydrogen bonds : bond 0.03892 / 4.01 ( 638) hydrogen bonds : angle 5.11969 / 6.54 ( 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 317 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9071 (tp) cc_final: 0.8786 (tp) REVERT: A 97 ASP cc_start: 0.7925 (t0) cc_final: 0.7580 (t0) REVERT: A 115 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 26 MET cc_start: 0.9168 (tpt) cc_final: 0.8734 (tpt) REVERT: B 62 SER cc_start: 0.8775 (t) cc_final: 0.8436 (p) REVERT: B 108 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: B 115 ASP cc_start: 0.8479 (m-30) cc_final: 0.7886 (t0) REVERT: B 182 MET cc_start: 0.8860 (ttp) cc_final: 0.8242 (ttp) REVERT: C 5 LYS cc_start: 0.6494 (tmtt) cc_final: 0.6012 (tmtt) REVERT: C 121 TYR cc_start: 0.8964 (t80) cc_final: 0.8112 (t80) REVERT: C 183 VAL cc_start: 0.8871 (m) cc_final: 0.8566 (p) REVERT: D 5 LYS cc_start: 0.8135 (mppt) cc_final: 0.7819 (mmtm) REVERT: D 38 MET cc_start: 0.8845 (mmt) cc_final: 0.8586 (mmp) REVERT: D 131 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8198 (ttt90) REVERT: E 202 SER cc_start: 0.9079 (p) cc_final: 0.8851 (p) REVERT: F 9 VAL cc_start: 0.8396 (t) cc_final: 0.8162 (p) REVERT: F 33 ASN cc_start: 0.8351 (p0) cc_final: 0.8008 (p0) REVERT: F 99 TYR cc_start: 0.8920 (t80) cc_final: 0.8699 (t80) REVERT: F 148 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: G 235 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8023 (p) REVERT: G 262 TYR cc_start: 0.8911 (m-80) cc_final: 0.8592 (m-80) REVERT: H 38 MET cc_start: 0.7729 (mmm) cc_final: 0.7113 (mmm) REVERT: H 118 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7247 (ttm170) REVERT: H 224 MET cc_start: 0.8368 (tpt) cc_final: 0.8143 (tpp) outliers start: 69 outliers final: 53 residues processed: 294 average time/residue: 0.1476 time to fit residues: 69.6507 Evaluate side-chains 297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 A residue 152 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS 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 35 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 245 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 131 ARG Chi-restraints excluded: chain D residue 183 VAL 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 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 172 MET 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 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 139 optimal weight: 4.9990 chunk 239 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN D 63 GLN D 146 ASN D 158 ASN F 63 GLN F 146 ASN F 148 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110502 restraints weight = 28982.146| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.89 r_work: 0.3092 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21691 Z= 0.226 Angle : 0.626 10.141 29972 Z= 0.342 Chirality : 0.047 0.420 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.311 174.330 4229 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.76 % Favored : 94.03 % Rotamer: Outliers : 4.18 % Allowed : 26.04 % 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: -1.72 (0.16), residues: 2379 helix: -0.55 (0.20), residues: 643 sheet: -0.77 (0.25), residues: 438 loop : -1.58 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 133 TYR 0.014 0.001 TYR H 117 PHE 0.027 0.002 PHE B 202 TRP 0.025 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (21690) covalent geometry : angle 0.62543 / 0.34 (29970) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 2.81265 / 3.77 ( 2) hydrogen bonds : bond 0.04017 / 4.17 ( 638) hydrogen bonds : angle 5.16209 / 6.55 ( 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 322 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 240 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8968 (tp) cc_final: 0.8659 (tp) REVERT: A 97 ASP cc_start: 0.7991 (t0) cc_final: 0.7599 (t0) REVERT: B 26 MET cc_start: 0.9224 (tpt) cc_final: 0.8797 (tpt) REVERT: B 62 SER cc_start: 0.8810 (t) cc_final: 0.8472 (p) REVERT: B 108 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: B 115 ASP cc_start: 0.8526 (m-30) cc_final: 0.7933 (t0) REVERT: B 182 MET cc_start: 0.8881 (ttp) cc_final: 0.8239 (ttp) REVERT: C 5 LYS cc_start: 0.6586 (tmtt) cc_final: 0.6056 (tmtt) REVERT: C 121 TYR cc_start: 0.9035 (t80) cc_final: 0.8198 (t80) REVERT: C 183 VAL cc_start: 0.8949 (m) cc_final: 0.8640 (p) REVERT: D 5 LYS cc_start: 0.8190 (mppt) cc_final: 0.7839 (mmtm) REVERT: D 38 MET cc_start: 0.8948 (mmt) cc_final: 0.8515 (mmp) REVERT: D 131 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8294 (ttt90) REVERT: D 227 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: F 9 VAL cc_start: 0.8510 (t) cc_final: 0.8270 (p) REVERT: F 33 ASN cc_start: 0.8395 (p0) cc_final: 0.8059 (p0) REVERT: F 99 TYR cc_start: 0.8948 (t80) cc_final: 0.8735 (t80) REVERT: F 148 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: G 235 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (p) REVERT: G 262 TYR cc_start: 0.9011 (m-80) cc_final: 0.8762 (m-80) REVERT: H 38 MET cc_start: 0.7756 (mmm) cc_final: 0.7133 (mmm) REVERT: H 224 MET cc_start: 0.8405 (tpt) cc_final: 0.8183 (tpp) outliers start: 82 outliers final: 71 residues processed: 296 average time/residue: 0.1546 time to fit residues: 72.5749 Evaluate side-chains 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 233 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 A residue 152 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS 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 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 88 ASP 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 114 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 33 ASN 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 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 172 MET 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 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 86 VAL Chi-restraints excluded: chain H residue 233 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 144 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN D 146 ASN D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 146 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 = 0.3926 r_free = 0.3926 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115195 restraints weight = 29011.337| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3142 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21691 Z= 0.146 Angle : 0.593 9.900 29972 Z= 0.324 Chirality : 0.045 0.418 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.304 174.884 4229 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.45 % Rotamer: Outliers : 3.67 % Allowed : 26.55 % 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: -1.61 (0.17), residues: 2379 helix: -0.45 (0.20), residues: 643 sheet: -0.84 (0.25), residues: 439 loop : -1.45 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.014 0.001 TYR H 117 PHE 0.019 0.001 PHE G 150 TRP 0.031 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (21690) covalent geometry : angle 0.59247 / 0.32 (29970) SS BOND : bond 0.00108 / 0.05 ( 1) SS BOND : angle 2.64061 / 3.70 ( 2) hydrogen bonds : bond 0.03858 / 4.01 ( 638) hydrogen bonds : angle 5.04430 / 6.40 ( 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 323 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.9006 (tp) cc_final: 0.8736 (tp) REVERT: A 97 ASP cc_start: 0.7973 (t0) cc_final: 0.7689 (t0) REVERT: A 115 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7997 (tp) REVERT: B 26 MET cc_start: 0.9106 (tpt) cc_final: 0.8724 (tpt) REVERT: B 108 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: B 115 ASP cc_start: 0.8349 (m-30) cc_final: 0.7950 (t0) REVERT: B 182 MET cc_start: 0.8694 (ttp) cc_final: 0.8180 (ttp) REVERT: C 5 LYS cc_start: 0.6698 (tmtt) cc_final: 0.6115 (tmtt) REVERT: C 121 TYR cc_start: 0.8912 (t80) cc_final: 0.8103 (t80) REVERT: C 168 GLU cc_start: 0.8456 (tt0) cc_final: 0.8245 (tt0) REVERT: C 183 VAL cc_start: 0.8839 (m) cc_final: 0.8590 (p) REVERT: D 5 LYS cc_start: 0.8107 (mppt) cc_final: 0.7885 (mmtm) REVERT: D 38 MET cc_start: 0.8757 (mmt) cc_final: 0.8424 (mmp) REVERT: D 131 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: D 227 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: E 13 SER cc_start: 0.8392 (m) cc_final: 0.8173 (m) REVERT: E 117 TYR cc_start: 0.8851 (t80) cc_final: 0.8619 (t80) REVERT: E 202 SER cc_start: 0.9022 (p) cc_final: 0.8812 (p) REVERT: F 9 VAL cc_start: 0.8342 (t) cc_final: 0.8127 (p) REVERT: F 33 ASN cc_start: 0.8323 (p0) cc_final: 0.7989 (p0) REVERT: F 148 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: G 235 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8180 (p) REVERT: H 38 MET cc_start: 0.7758 (mmm) cc_final: 0.7141 (mmm) REVERT: H 119 TYR cc_start: 0.7790 (m-10) cc_final: 0.7544 (m-10) outliers start: 72 outliers final: 57 residues processed: 299 average time/residue: 0.1487 time to fit residues: 71.7434 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS 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 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 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 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 33 ASN 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 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 172 MET 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 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 23 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 202 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN 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** ** 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 = 0.3939 r_free = 0.3939 target = 0.159042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116669 restraints weight = 29157.422| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.76 r_work: 0.3170 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21691 Z= 0.136 Angle : 0.586 9.732 29972 Z= 0.321 Chirality : 0.045 0.416 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.271 175.097 4229 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.58 % Rotamer: Outliers : 3.21 % Allowed : 26.86 % Favored : 69.93 % 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: -1.50 (0.17), residues: 2379 helix: -0.35 (0.20), residues: 645 sheet: -0.83 (0.25), residues: 427 loop : -1.38 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 133 TYR 0.026 0.001 TYR H 81 PHE 0.028 0.001 PHE B 202 TRP 0.042 0.001 TRP H 239 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (21690) covalent geometry : angle 0.58413 / 0.32 (29970) SS BOND : bond 0.01632 / 0.82 ( 1) SS BOND : angle 5.43802 / 10.71 ( 2) hydrogen bonds : bond 0.03708 / 3.82 ( 638) hydrogen bonds : angle 4.95560 / 6.31 ( 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 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8992 (tp) cc_final: 0.8726 (tp) REVERT: A 97 ASP cc_start: 0.7959 (t0) cc_final: 0.7686 (t0) REVERT: B 26 MET cc_start: 0.9070 (tpt) cc_final: 0.8739 (tpt) REVERT: B 108 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: B 115 ASP cc_start: 0.8300 (m-30) cc_final: 0.7938 (t0) REVERT: B 182 MET cc_start: 0.8676 (ttp) cc_final: 0.8229 (ttp) REVERT: C 5 LYS cc_start: 0.6754 (tmtt) cc_final: 0.6153 (tmtt) REVERT: C 121 TYR cc_start: 0.8888 (t80) cc_final: 0.8141 (t80) REVERT: C 183 VAL cc_start: 0.8790 (m) cc_final: 0.8537 (p) REVERT: D 5 LYS cc_start: 0.8087 (mppt) cc_final: 0.7853 (mmtm) REVERT: D 38 MET cc_start: 0.8670 (mmt) cc_final: 0.8373 (mmp) REVERT: D 131 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8209 (ttt90) REVERT: D 227 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: E 13 SER cc_start: 0.8415 (m) cc_final: 0.8207 (m) REVERT: E 117 TYR cc_start: 0.8759 (t80) cc_final: 0.8521 (t80) REVERT: E 202 SER cc_start: 0.9012 (p) cc_final: 0.8777 (p) REVERT: F 9 VAL cc_start: 0.8224 (t) cc_final: 0.7983 (p) REVERT: F 33 ASN cc_start: 0.8284 (p0) cc_final: 0.7949 (p0) REVERT: G 235 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8110 (p) REVERT: H 38 MET cc_start: 0.7721 (mmm) cc_final: 0.7100 (mmm) REVERT: H 118 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6484 (ttp-110) REVERT: H 169 ILE cc_start: 0.6943 (tt) cc_final: 0.6633 (tp) outliers start: 63 outliers final: 55 residues processed: 288 average time/residue: 0.1440 time to fit residues: 67.3684 Evaluate side-chains 301 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS 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 88 ASP 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 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 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 33 ASN 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 88 ASP 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 172 MET 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 199 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 55 optimal weight: 0.2980 chunk 196 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 171 optimal weight: 0.0270 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.158913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116669 restraints weight = 29133.853| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.76 r_work: 0.3160 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 21691 Z= 0.179 Angle : 0.736 59.183 29972 Z= 0.425 Chirality : 0.048 1.091 3474 Planarity : 0.005 0.131 3433 Dihedral : 21.270 175.099 4229 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 3.26 % Allowed : 27.06 % Favored : 69.67 % Cbeta Deviations : 0.05 % 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: -1.50 (0.17), residues: 2379 helix: -0.34 (0.20), residues: 645 sheet: -0.81 (0.25), residues: 421 loop : -1.39 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 133 TYR 0.022 0.001 TYR H 81 PHE 0.026 0.001 PHE B 202 TRP 0.035 0.001 TRP H 239 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (21690) covalent geometry : angle 0.73501 / 0.42 (29970) SS BOND : bond 0.00915 / 0.46 ( 1) SS BOND : angle 5.13279 / 9.66 ( 2) hydrogen bonds : bond 0.03716 / 3.82 ( 638) hydrogen bonds : angle 4.95641 / 6.31 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6175.19 seconds wall clock time: 106 minutes 36.48 seconds (6396.48 seconds total)