Starting phenix.real_space_refine on Thu Jul 2 18:38:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jia_36304/07_2026/8jia_36304.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 6 5.49 5 S 49 5.16 5 C 6045 2.51 5 N 1697 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9587 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1581 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 9, 'TRANS': 217} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 13, 'ASP:plan': 5, 'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1576 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "E" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1884 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 8, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR%COO:plan': 1} Unresolved non-hydrogen planarities: 164 Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2227 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2257 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.21 Number of scatterers: 9587 At special positions: 0 Unit cell: (119.78, 106, 193.98, 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 49 16.00 P 6 15.00 O 1790 8.00 N 1697 7.00 C 6045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 78 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 379.8 milliseconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 50.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.642A pdb=" N LEU A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.590A pdb=" N LEU A 79 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.949A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.517A pdb=" N VAL A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.625A pdb=" N GLN A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.657A pdb=" N MET A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.554A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 206' Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.659A pdb=" N LEU B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.682A pdb=" N VAL B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 141 through 153 removed outlier: 3.875A pdb=" N GLN B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.015A pdb=" N ARG B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 110 removed outlier: 3.924A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 66 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.759A pdb=" N ILE E 122 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 195 removed outlier: 3.735A pdb=" N ILE E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E 195 " --> pdb=" O GLN E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 202 Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.664A pdb=" N ASN D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 50 removed outlier: 3.516A pdb=" N THR D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.925A pdb=" N ALA D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.707A pdb=" N ASP D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.409A pdb=" N PHE D 122 " --> pdb=" O LYS D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.672A pdb=" N ASP D 140 " --> pdb=" O HIS D 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 141' Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 164 through 190 removed outlier: 3.587A pdb=" N GLY D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 196 removed outlier: 3.762A pdb=" N VAL D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.678A pdb=" N ILE D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 244 removed outlier: 4.481A pdb=" N GLN D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 218 " --> pdb=" O TRP D 214 " (cutoff:3.500A) Proline residue: D 219 - end of helix removed outlier: 3.839A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 264 through 271 removed outlier: 3.747A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 285 Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.517A pdb=" N ARG D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 293' Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.896A pdb=" N GLY C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN C 17 " --> pdb=" O GLY C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 49 removed outlier: 3.618A pdb=" N ILE C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 removed outlier: 3.846A pdb=" N ASN C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.827A pdb=" N LYS C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.203A pdb=" N TYR C 103 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 161 through 199 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.677A pdb=" N GLY C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 247 removed outlier: 3.798A pdb=" N GLN C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 4.220A pdb=" N PHE C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.843A pdb=" N GLN C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 4.081A pdb=" N ALA C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9 removed outlier: 6.266A pdb=" N HIS A 7 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP A 60 " --> pdb=" O HIS A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 5.659A pdb=" N GLY A 84 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP A 164 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 86 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE A 34 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU A 212 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 209 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP A 220 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU A 211 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 9 removed outlier: 3.590A pdb=" N ARG B 62 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP B 6 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 60 " --> pdb=" O ASP B 6 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 8 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B 58 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 5.788A pdb=" N GLY B 84 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.134A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3169 1.34 - 1.46: 1871 1.46 - 1.58: 4586 1.58 - 1.70: 7 1.70 - 1.82: 91 Bond restraints: 9724 Sorted by residual: bond pdb=" CA ASN D 17 " pdb=" CB ASN D 17 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.27e-02 6.20e+03 5.26e+00 bond pdb=" CA ILE A 23 " pdb=" CB ILE A 23 " ideal model delta sigma weight residual 1.539 1.558 -0.020 1.19e-02 7.06e+03 2.73e+00 bond pdb=" C VAL B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.25e-02 6.40e+03 2.58e+00 bond pdb=" CB GLN B 95 " pdb=" CG GLN B 95 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" C VAL A 120 " pdb=" N PRO A 121 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.37e+00 ... (remaining 9719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 12888 2.79 - 5.58: 278 5.58 - 8.37: 63 8.37 - 11.16: 14 11.16 - 13.94: 4 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N VAL E 304 " pdb=" CA VAL E 304 " pdb=" C VAL E 304 " ideal model delta sigma weight residual 113.71 108.30 5.41 9.50e-01 1.11e+00 3.24e+01 angle pdb=" CB MET D 225 " pdb=" CG MET D 225 " pdb=" SD MET D 225 " ideal model delta sigma weight residual 112.70 126.64 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C ASP B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" N ILE A 185 " pdb=" CA ILE A 185 " pdb=" C ILE A 185 " ideal model delta sigma weight residual 112.35 106.08 6.27 1.41e+00 5.03e-01 1.98e+01 angle pdb=" N VAL D 242 " pdb=" CA VAL D 242 " pdb=" C VAL D 242 " ideal model delta sigma weight residual 113.39 106.88 6.51 1.47e+00 4.63e-01 1.96e+01 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 5388 15.89 - 31.78: 352 31.78 - 47.68: 67 47.68 - 63.57: 12 63.57 - 79.46: 4 Dihedral angle restraints: 5823 sinusoidal: 2005 harmonic: 3818 Sorted by residual: dihedral pdb=" CA LYS C 262 " pdb=" C LYS C 262 " pdb=" N VAL C 263 " pdb=" CA VAL C 263 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA MET D 206 " pdb=" C MET D 206 " pdb=" N ARG D 207 " pdb=" CA ARG D 207 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ILE C 85 " pdb=" C ILE C 85 " pdb=" N GLU C 86 " pdb=" CA GLU C 86 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.106: 377 0.106 - 0.159: 82 0.159 - 0.212: 20 0.212 - 0.265: 5 Chirality restraints: 1621 Sorted by residual: chirality pdb=" CG LEU D 239 " pdb=" CB LEU D 239 " pdb=" CD1 LEU D 239 " pdb=" CD2 LEU D 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL B 76 " pdb=" CA VAL B 76 " pdb=" CG1 VAL B 76 " pdb=" CG2 VAL B 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR A 167 " pdb=" CA THR A 167 " pdb=" OG1 THR A 167 " pdb=" CG2 THR A 167 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1618 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 110 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO C 111 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 57 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.40e+00 pdb=" CD GLU D 57 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU D 57 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 57 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 223 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" CD GLU C 223 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU C 223 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 223 " 0.011 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2958 2.82 - 3.34: 9285 3.34 - 3.86: 15527 3.86 - 4.38: 17074 4.38 - 4.90: 28606 Nonbonded interactions: 73450 Sorted by model distance: nonbonded pdb=" O LEU E 47 " pdb=" OG1 THR E 363 " model vdw 2.306 3.040 nonbonded pdb=" O ARG C 213 " pdb=" OG1 THR C 216 " model vdw 2.325 3.040 nonbonded pdb=" O ILE C 268 " pdb=" OG1 THR C 272 " model vdw 2.329 3.040 nonbonded pdb=" O GLU C 9 " pdb=" OG1 THR C 12 " model vdw 2.336 3.040 nonbonded pdb=" NH1 ARG C 99 " pdb=" OD1 ASP C 120 " model vdw 2.356 3.120 ... (remaining 73445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 12 or (resid 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 or (resid \ 24 and (name N or name CA or name C or name O or name CB )) or resid 25 or (res \ id 26 and (name N or name CA or name C or name O or name CB )) or resid 27 or (r \ esid 28 through 29 and (name N or name CA or name C or name O or name CB )) or r \ esid 30 through 65 or (resid 66 through 70 and (name N or name CA or name C or n \ ame O or name CB )) or resid 71 through 88 or (resid 89 and (name N or name CA o \ r name C or name O or name CB )) or resid 90 through 92 or (resid 93 through 100 \ and (name N or name CA or name C or name O or name CB )) or resid 101 through 1 \ 24 or (resid 125 and (name N or name CA or name C or name O or name CB )) or res \ id 126 through 133 or (resid 134 through 136 and (name N or name CA or name C or \ name O or name CB )) or resid 137 through 138 or (resid 139 and (name N or name \ CA or name C or name O or name CB )) or resid 140 through 172 or (resid 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 217 o \ r (resid 218 through 219 and (name N or name CA or name C or name O or name CB ) \ ) or resid 220 through 225 or resid 301)) selection = (chain 'B' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or (resid 30 through 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 34 or (resid 35 through 36 and (na \ me N or name CA or name C or name O or name CB )) or resid 37 through 44 or (res \ id 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ gh 50 or (resid 51 through 55 and (name N or name CA or name C or name O or name \ CB )) or resid 56 through 59 or (resid 60 and (name N or name CA or name C or n \ ame O or name CB )) or resid 61 through 68 or (resid 69 through 70 and (name N o \ r name CA or name C or name O or name CB )) or resid 71 or (resid 72 and (name N \ or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and (name \ N or name CA or name C or name O or name CB )) or resid 75 through 77 or (resid \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 94 or (resid 95 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 128 or (resid 129 and (name N or name CA or name C or \ name O or name CB )) or resid 130 through 137 or (resid 138 through 139 and (na \ me N or name CA or name C or name O or name CB )) or resid 140 through 156 or (r \ esid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or resid 177 through 179 or (resid 180 and (name N or name CA or name C or nam \ e O or name CB )) or resid 181 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 through 198 or (resid 199 and (na \ me N or name CA or name C or name O or name CB )) or resid 200 through 213 or (r \ esid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 t \ hrough 218 or (resid 219 and (name N or name CA or name C or name O or name CB ) \ ) or resid 220 or (resid 221 through 223 and (name N or name CA or name C or nam \ e O or name CB )) or resid 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 301)) } ncs_group { reference = (chain 'C' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 133 or \ (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 or (resid 137 and (name N or name CA or name C or name O or name C \ B )) or resid 138 through 152 or (resid 153 through 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 219 or (resid 220 and (nam \ e N or name CA or name C or name O or name CB )) or resid 221 through 291 or (re \ sid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5)) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 143 or (resid 144 an \ d (name N or name CA or name C or name O or name CB )) or resid 145 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 through 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.005 0.076 9726 Z= 0.220 Angle : 1.062 13.944 13251 Z= 0.546 Chirality : 0.056 0.265 1621 Planarity : 0.006 0.074 1710 Dihedral : 11.585 79.459 3341 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.15 % Favored : 92.62 % Rotamer: Outliers : 0.33 % Allowed : 0.99 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.20), residues: 1315 helix: -1.72 (0.18), residues: 585 sheet: -2.20 (0.66), residues: 54 loop : -2.50 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 187 TYR 0.028 0.002 TYR C 255 PHE 0.019 0.002 PHE D 110 TRP 0.006 0.001 TRP C 274 HIS 0.016 0.002 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 ( 9724) covalent geometry : angle 1.06159 / 0.55 (13247) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.79358 / 0.29 ( 4) hydrogen bonds : bond 0.17955 / 12.26 ( 410) hydrogen bonds : angle 6.65607 / 4.85 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8601 (t) cc_final: 0.8396 (t) REVERT: B 205 MET cc_start: 0.8013 (mmp) cc_final: 0.7464 (mmp) REVERT: E 52 ARG cc_start: 0.8165 (tpm170) cc_final: 0.7459 (tpp-160) REVERT: E 305 MET cc_start: 0.8275 (tmm) cc_final: 0.7915 (tmm) REVERT: E 358 MET cc_start: 0.6550 (mpp) cc_final: 0.6061 (mpp) REVERT: D 157 GLU cc_start: 0.7976 (pm20) cc_final: 0.7702 (pm20) REVERT: D 160 ASP cc_start: 0.8499 (m-30) cc_final: 0.7963 (t0) REVERT: D 217 GLN cc_start: 0.8793 (pm20) cc_final: 0.8478 (pm20) REVERT: D 252 ASN cc_start: 0.8506 (m110) cc_final: 0.7096 (m-40) REVERT: D 282 MET cc_start: 0.8482 (ppp) cc_final: 0.8203 (ppp) REVERT: C 230 MET cc_start: 0.9007 (tpt) cc_final: 0.8681 (tpp) REVERT: C 255 TYR cc_start: 0.8152 (t80) cc_final: 0.7500 (t80) REVERT: C 262 LYS cc_start: 0.8854 (mmpt) cc_final: 0.8587 (mmtt) REVERT: C 278 LEU cc_start: 0.9308 (tp) cc_final: 0.9107 (tt) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.0651 time to fit residues: 17.1528 Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN E 48 ASN E 100 GLN E 104 ASN E 117 HIS D 100 GLN D 101 GLN D 112 GLN C 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058920 restraints weight = 51764.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060325 restraints weight = 31285.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061136 restraints weight = 21910.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061885 restraints weight = 17457.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062319 restraints weight = 14372.280| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9726 Z= 0.112 Angle : 0.593 7.462 13251 Z= 0.303 Chirality : 0.040 0.131 1621 Planarity : 0.004 0.046 1710 Dihedral : 4.713 57.410 1416 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 1.10 % Allowed : 10.00 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.22), residues: 1315 helix: -0.28 (0.20), residues: 632 sheet: -2.95 (0.56), residues: 63 loop : -2.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.008 0.001 TYR C 294 PHE 0.017 0.001 PHE A 87 TRP 0.004 0.001 TRP D 214 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9724) covalent geometry : angle 0.59254 / 0.30 (13247) SS BOND : bond 0.00251 / 0.13 ( 2) SS BOND : angle 0.48749 / 0.20 ( 4) hydrogen bonds : bond 0.03967 / 2.68 ( 410) hydrogen bonds : angle 4.45999 / 3.21 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8730 (m-10) cc_final: 0.8394 (m-10) REVERT: A 187 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8071 (mtm-85) REVERT: B 205 MET cc_start: 0.7930 (mmp) cc_final: 0.7545 (mmp) REVERT: E 52 ARG cc_start: 0.8285 (tpm170) cc_final: 0.7488 (tpm170) REVERT: E 305 MET cc_start: 0.8457 (tmm) cc_final: 0.8127 (tmm) REVERT: D 160 ASP cc_start: 0.8532 (m-30) cc_final: 0.8031 (t0) REVERT: D 190 ASN cc_start: 0.8763 (p0) cc_final: 0.8160 (p0) REVERT: D 217 GLN cc_start: 0.8796 (pm20) cc_final: 0.8584 (pm20) REVERT: D 223 GLU cc_start: 0.8628 (pm20) cc_final: 0.8337 (pm20) REVERT: D 248 GLU cc_start: 0.7625 (tp30) cc_final: 0.7300 (tp30) REVERT: D 252 ASN cc_start: 0.8476 (m110) cc_final: 0.7103 (m110) REVERT: D 282 MET cc_start: 0.8479 (ppp) cc_final: 0.8037 (ppp) REVERT: C 214 TRP cc_start: 0.8084 (t-100) cc_final: 0.7870 (t60) REVERT: C 278 LEU cc_start: 0.9303 (tp) cc_final: 0.9076 (tt) outliers start: 10 outliers final: 4 residues processed: 164 average time/residue: 0.0676 time to fit residues: 16.3836 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.071245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056868 restraints weight = 52559.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058277 restraints weight = 31309.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059217 restraints weight = 21818.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059878 restraints weight = 16834.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060115 restraints weight = 14048.769| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9726 Z= 0.125 Angle : 0.581 9.798 13251 Z= 0.294 Chirality : 0.040 0.139 1621 Planarity : 0.003 0.047 1710 Dihedral : 4.184 35.815 1414 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.92 % Favored : 92.78 % Rotamer: Outliers : 1.21 % Allowed : 14.73 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1315 helix: 0.29 (0.21), residues: 637 sheet: -2.34 (0.63), residues: 62 loop : -2.10 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 187 TYR 0.009 0.001 TYR C 255 PHE 0.017 0.001 PHE A 87 TRP 0.007 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9724) covalent geometry : angle 0.58074 / 0.29 (13247) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.40150 / 0.15 ( 4) hydrogen bonds : bond 0.03622 / 2.47 ( 410) hydrogen bonds : angle 4.15709 / 2.98 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8678 (m-10) cc_final: 0.8373 (m-10) REVERT: B 205 MET cc_start: 0.8000 (mmp) cc_final: 0.7683 (mmm) REVERT: E 52 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7593 (tpm170) REVERT: E 305 MET cc_start: 0.8496 (tmm) cc_final: 0.8184 (tmm) REVERT: D 160 ASP cc_start: 0.8427 (m-30) cc_final: 0.7949 (t0) REVERT: D 171 ASN cc_start: 0.8181 (p0) cc_final: 0.7838 (p0) REVERT: D 180 GLN cc_start: 0.8903 (tp40) cc_final: 0.8667 (tp-100) REVERT: D 248 GLU cc_start: 0.7638 (tp30) cc_final: 0.7135 (tp30) REVERT: D 252 ASN cc_start: 0.8557 (m110) cc_final: 0.7167 (m110) REVERT: D 282 MET cc_start: 0.8479 (ppp) cc_final: 0.7977 (ppp) REVERT: C 214 TRP cc_start: 0.8173 (t-100) cc_final: 0.7836 (t60) outliers start: 11 outliers final: 4 residues processed: 152 average time/residue: 0.0700 time to fit residues: 15.7005 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 0.0000 chunk 74 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 189 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.070894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055878 restraints weight = 54050.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057236 restraints weight = 32841.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058198 restraints weight = 23154.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058617 restraints weight = 17956.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059206 restraints weight = 15482.896| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9726 Z= 0.128 Angle : 0.566 7.335 13251 Z= 0.288 Chirality : 0.040 0.140 1621 Planarity : 0.003 0.048 1710 Dihedral : 4.123 39.342 1414 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.69 % Favored : 93.08 % Rotamer: Outliers : 1.54 % Allowed : 16.26 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1315 helix: 0.56 (0.21), residues: 644 sheet: -2.24 (0.67), residues: 60 loop : -2.03 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.014 0.001 TYR C 294 PHE 0.012 0.001 PHE C 246 TRP 0.006 0.001 TRP C 274 HIS 0.002 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9724) covalent geometry : angle 0.56571 / 0.29 (13247) SS BOND : bond 0.00169 / 0.09 ( 2) SS BOND : angle 0.52678 / 0.19 ( 4) hydrogen bonds : bond 0.03498 / 2.37 ( 410) hydrogen bonds : angle 3.98242 / 2.86 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8692 (m-10) cc_final: 0.8370 (m-10) REVERT: B 205 MET cc_start: 0.8086 (mmp) cc_final: 0.7767 (mmm) REVERT: E 46 LYS cc_start: 0.3739 (OUTLIER) cc_final: 0.3395 (pptt) REVERT: E 52 ARG cc_start: 0.8489 (tpm170) cc_final: 0.7932 (tpp-160) REVERT: E 305 MET cc_start: 0.8476 (tmm) cc_final: 0.8230 (tmm) REVERT: D 160 ASP cc_start: 0.8531 (m-30) cc_final: 0.8073 (t0) REVERT: D 180 GLN cc_start: 0.9006 (tp40) cc_final: 0.8772 (tp-100) REVERT: D 223 GLU cc_start: 0.8579 (pm20) cc_final: 0.8343 (pm20) REVERT: D 248 GLU cc_start: 0.7771 (tp30) cc_final: 0.7270 (tp30) REVERT: D 252 ASN cc_start: 0.8681 (m110) cc_final: 0.7167 (m110) REVERT: D 282 MET cc_start: 0.8475 (ppp) cc_final: 0.7970 (ppp) REVERT: C 214 TRP cc_start: 0.8174 (t-100) cc_final: 0.7819 (t60) outliers start: 14 outliers final: 7 residues processed: 150 average time/residue: 0.0839 time to fit residues: 18.1852 Evaluate side-chains 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 0.0050 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 65 GLN E 69 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN C 146 GLN C 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052627 restraints weight = 54447.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053734 restraints weight = 33580.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054728 restraints weight = 21699.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054799 restraints weight = 17959.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054870 restraints weight = 16110.389| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9726 Z= 0.221 Angle : 0.658 7.313 13251 Z= 0.342 Chirality : 0.043 0.161 1621 Planarity : 0.004 0.042 1710 Dihedral : 4.662 44.727 1414 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.60 % Favored : 92.17 % Rotamer: Outliers : 2.09 % Allowed : 17.03 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.24), residues: 1315 helix: 0.30 (0.21), residues: 669 sheet: -1.64 (0.69), residues: 62 loop : -1.94 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 55 TYR 0.013 0.002 TYR B 12 PHE 0.018 0.002 PHE C 126 TRP 0.012 0.001 TRP C 274 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 9724) covalent geometry : angle 0.65800 / 0.34 (13247) SS BOND : bond 0.00284 / 0.15 ( 2) SS BOND : angle 0.94530 / 0.34 ( 4) hydrogen bonds : bond 0.03822 / 2.59 ( 410) hydrogen bonds : angle 4.23313 / 3.06 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8791 (m-10) cc_final: 0.8378 (m-10) REVERT: B 205 MET cc_start: 0.8321 (mmp) cc_final: 0.7933 (mmm) REVERT: E 46 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3563 (pptt) REVERT: E 52 ARG cc_start: 0.8478 (tpm170) cc_final: 0.7891 (tpp-160) REVERT: E 305 MET cc_start: 0.8323 (tmm) cc_final: 0.8115 (tmm) REVERT: D 160 ASP cc_start: 0.8396 (m-30) cc_final: 0.7926 (t0) REVERT: D 223 GLU cc_start: 0.8557 (pm20) cc_final: 0.8105 (pm20) REVERT: D 248 GLU cc_start: 0.7682 (tp30) cc_final: 0.7107 (tp30) REVERT: D 252 ASN cc_start: 0.8838 (m110) cc_final: 0.7251 (m110) REVERT: D 282 MET cc_start: 0.8376 (ppp) cc_final: 0.8053 (ppp) REVERT: C 54 ASP cc_start: 0.7107 (p0) cc_final: 0.6882 (p0) REVERT: C 241 VAL cc_start: 0.9555 (m) cc_final: 0.9301 (p) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.0788 time to fit residues: 16.9579 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** C 190 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 = 0.3439 r_free = 0.3439 target = 0.066017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051492 restraints weight = 54671.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.052754 restraints weight = 32805.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053611 restraints weight = 23094.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054206 restraints weight = 18075.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054489 restraints weight = 15168.249| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9726 Z= 0.201 Angle : 0.656 10.684 13251 Z= 0.338 Chirality : 0.043 0.161 1621 Planarity : 0.004 0.052 1710 Dihedral : 4.690 45.574 1414 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.45 % Favored : 92.32 % Rotamer: Outliers : 1.98 % Allowed : 18.57 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1315 helix: 0.32 (0.21), residues: 667 sheet: -1.61 (0.70), residues: 62 loop : -1.91 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 55 TYR 0.010 0.001 TYR C 255 PHE 0.017 0.001 PHE C 126 TRP 0.009 0.001 TRP C 274 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 9724) covalent geometry : angle 0.65625 / 0.34 (13247) SS BOND : bond 0.00290 / 0.15 ( 2) SS BOND : angle 0.90202 / 0.34 ( 4) hydrogen bonds : bond 0.03815 / 2.56 ( 410) hydrogen bonds : angle 4.25847 / 3.05 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8810 (m-80) cc_final: 0.8390 (m-10) REVERT: A 179 MET cc_start: 0.9059 (mmp) cc_final: 0.8792 (mmp) REVERT: B 183 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8162 (tm-30) REVERT: B 205 MET cc_start: 0.8355 (mmp) cc_final: 0.7954 (mmm) REVERT: E 46 LYS cc_start: 0.4041 (OUTLIER) cc_final: 0.3624 (pptt) REVERT: E 52 ARG cc_start: 0.8560 (tpm170) cc_final: 0.7988 (tpp-160) REVERT: E 112 MET cc_start: 0.8723 (mpp) cc_final: 0.8407 (mpp) REVERT: D 223 GLU cc_start: 0.8634 (pm20) cc_final: 0.8150 (pm20) REVERT: D 248 GLU cc_start: 0.7688 (tp30) cc_final: 0.7454 (tp30) REVERT: D 282 MET cc_start: 0.8368 (ppp) cc_final: 0.7760 (ppp) REVERT: C 215 TYR cc_start: 0.8104 (t80) cc_final: 0.7767 (t80) REVERT: C 241 VAL cc_start: 0.9547 (m) cc_final: 0.9272 (p) REVERT: C 288 TYR cc_start: 0.8322 (t80) cc_final: 0.8078 (t80) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.0784 time to fit residues: 16.9584 Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.053446 restraints weight = 53357.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054772 restraints weight = 31969.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055683 restraints weight = 22497.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056315 restraints weight = 17614.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056631 restraints weight = 14781.163| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9726 Z= 0.117 Angle : 0.612 9.778 13251 Z= 0.308 Chirality : 0.041 0.174 1621 Planarity : 0.004 0.058 1710 Dihedral : 4.435 44.083 1414 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.92 % Favored : 92.85 % Rotamer: Outliers : 1.21 % Allowed : 20.11 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.24), residues: 1315 helix: 0.48 (0.21), residues: 667 sheet: -1.59 (0.68), residues: 64 loop : -1.98 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.006 0.001 TYR C 255 PHE 0.009 0.001 PHE C 126 TRP 0.006 0.001 TRP E 306 HIS 0.002 0.000 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9724) covalent geometry : angle 0.61167 / 0.31 (13247) SS BOND : bond 0.00211 / 0.11 ( 2) SS BOND : angle 0.62684 / 0.25 ( 4) hydrogen bonds : bond 0.03547 / 2.39 ( 410) hydrogen bonds : angle 3.99504 / 2.85 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8793 (m-80) cc_final: 0.8508 (m-10) REVERT: A 179 MET cc_start: 0.9052 (mmp) cc_final: 0.8847 (mmp) REVERT: B 162 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8618 (pt) REVERT: B 183 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 205 MET cc_start: 0.8079 (mmp) cc_final: 0.7689 (mmm) REVERT: E 46 LYS cc_start: 0.4091 (OUTLIER) cc_final: 0.3728 (pptt) REVERT: E 52 ARG cc_start: 0.8529 (tpm170) cc_final: 0.7919 (tpm170) REVERT: E 112 MET cc_start: 0.8660 (mpp) cc_final: 0.8303 (mpp) REVERT: E 141 MET cc_start: 0.9074 (tpp) cc_final: 0.8836 (tpt) REVERT: E 352 TYR cc_start: 0.7185 (m-80) cc_final: 0.6924 (m-80) REVERT: D 24 MET cc_start: 0.8271 (tpp) cc_final: 0.7956 (ttm) REVERT: D 157 GLU cc_start: 0.7749 (pm20) cc_final: 0.7522 (pm20) REVERT: D 160 ASP cc_start: 0.8013 (m-30) cc_final: 0.7220 (t0) REVERT: D 248 GLU cc_start: 0.7708 (tp30) cc_final: 0.7358 (tp30) REVERT: D 252 ASN cc_start: 0.8840 (m110) cc_final: 0.7052 (m-40) REVERT: D 282 MET cc_start: 0.8312 (ppp) cc_final: 0.7839 (ppp) REVERT: C 214 TRP cc_start: 0.8113 (t-100) cc_final: 0.7807 (t60) REVERT: C 215 TYR cc_start: 0.8036 (t80) cc_final: 0.7760 (t80) REVERT: C 241 VAL cc_start: 0.9537 (m) cc_final: 0.9254 (p) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.0780 time to fit residues: 17.2770 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 17 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.068514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053713 restraints weight = 53805.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055063 restraints weight = 31971.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055996 restraints weight = 22334.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056547 restraints weight = 17371.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057028 restraints weight = 14715.420| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9726 Z= 0.123 Angle : 0.627 8.351 13251 Z= 0.316 Chirality : 0.041 0.196 1621 Planarity : 0.004 0.054 1710 Dihedral : 4.309 42.810 1414 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.92 % Favored : 92.85 % Rotamer: Outliers : 1.87 % Allowed : 20.33 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1315 helix: 0.61 (0.21), residues: 656 sheet: -1.40 (0.71), residues: 62 loop : -1.92 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.006 0.001 TYR C 294 PHE 0.009 0.001 PHE A 90 TRP 0.008 0.001 TRP E 306 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9724) covalent geometry : angle 0.62692 / 0.32 (13247) SS BOND : bond 0.00213 / 0.11 ( 2) SS BOND : angle 0.56222 / 0.24 ( 4) hydrogen bonds : bond 0.03488 / 2.35 ( 410) hydrogen bonds : angle 3.93274 / 2.79 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8786 (m-80) cc_final: 0.8491 (m-10) REVERT: B 47 MET cc_start: 0.9144 (mmp) cc_final: 0.8936 (mmp) REVERT: B 183 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8158 (tm-30) REVERT: B 205 MET cc_start: 0.8040 (mmp) cc_final: 0.7638 (mmm) REVERT: E 46 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3803 (pptt) REVERT: E 48 ASN cc_start: 0.8809 (t0) cc_final: 0.8423 (p0) REVERT: E 52 ARG cc_start: 0.8520 (tpm170) cc_final: 0.7902 (tpp-160) REVERT: E 112 MET cc_start: 0.8652 (mpp) cc_final: 0.8279 (mpp) REVERT: E 141 MET cc_start: 0.9060 (tpp) cc_final: 0.8830 (tpt) REVERT: D 24 MET cc_start: 0.8279 (tpp) cc_final: 0.8062 (ttm) REVERT: D 157 GLU cc_start: 0.7774 (pm20) cc_final: 0.7555 (pm20) REVERT: D 160 ASP cc_start: 0.8038 (m-30) cc_final: 0.7258 (t0) REVERT: D 248 GLU cc_start: 0.7679 (tp30) cc_final: 0.7331 (tp30) REVERT: D 252 ASN cc_start: 0.8830 (m110) cc_final: 0.7028 (m-40) REVERT: D 282 MET cc_start: 0.8349 (ppp) cc_final: 0.7985 (ppp) REVERT: C 54 ASP cc_start: 0.6306 (p0) cc_final: 0.6090 (p0) REVERT: C 214 TRP cc_start: 0.8068 (t-100) cc_final: 0.7817 (t60) REVERT: C 215 TYR cc_start: 0.8030 (t80) cc_final: 0.7788 (t80) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 0.0798 time to fit residues: 18.2033 Evaluate side-chains 137 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.050810 restraints weight = 54263.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052057 restraints weight = 32171.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052736 restraints weight = 22415.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053307 restraints weight = 17994.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053792 restraints weight = 14989.497| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9726 Z= 0.236 Angle : 0.745 11.500 13251 Z= 0.377 Chirality : 0.046 0.301 1621 Planarity : 0.004 0.051 1710 Dihedral : 4.771 44.966 1414 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.59 % Favored : 91.18 % Rotamer: Outliers : 2.09 % Allowed : 21.10 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1315 helix: 0.45 (0.21), residues: 665 sheet: -1.55 (0.64), residues: 80 loop : -1.94 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 55 TYR 0.012 0.002 TYR B 12 PHE 0.020 0.002 PHE C 163 TRP 0.012 0.002 TRP C 274 HIS 0.005 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 ( 9724) covalent geometry : angle 0.74530 / 0.38 (13247) SS BOND : bond 0.00365 / 0.19 ( 2) SS BOND : angle 0.89507 / 0.36 ( 4) hydrogen bonds : bond 0.03922 / 2.66 ( 410) hydrogen bonds : angle 4.30048 / 3.07 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8843 (m-80) cc_final: 0.8492 (m-10) REVERT: A 179 MET cc_start: 0.9177 (mmp) cc_final: 0.8959 (mmp) REVERT: B 162 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8696 (pt) REVERT: B 205 MET cc_start: 0.8328 (mmp) cc_final: 0.7931 (mmm) REVERT: B 212 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8435 (tt) REVERT: E 46 LYS cc_start: 0.4316 (OUTLIER) cc_final: 0.3874 (pptt) REVERT: E 52 ARG cc_start: 0.8556 (tpm170) cc_final: 0.7973 (tpp-160) REVERT: E 190 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8846 (mmtt) REVERT: D 144 LYS cc_start: 0.8209 (pptt) cc_final: 0.7712 (mmmt) REVERT: D 248 GLU cc_start: 0.7712 (tp30) cc_final: 0.7438 (tp30) REVERT: C 215 TYR cc_start: 0.8085 (t80) cc_final: 0.7877 (t80) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.0790 time to fit residues: 15.9400 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain C residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 0.9980 chunk 127 optimal weight: 0.0270 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053001 restraints weight = 53359.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054334 restraints weight = 31772.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055256 restraints weight = 22218.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055792 restraints weight = 17270.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055999 restraints weight = 14685.550| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9726 Z= 0.126 Angle : 0.681 12.402 13251 Z= 0.334 Chirality : 0.043 0.266 1621 Planarity : 0.004 0.064 1710 Dihedral : 4.488 44.058 1414 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.69 % Favored : 93.08 % Rotamer: Outliers : 1.54 % Allowed : 22.09 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1315 helix: 0.59 (0.21), residues: 660 sheet: -1.22 (0.73), residues: 62 loop : -2.01 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 243 TYR 0.005 0.001 TYR C 294 PHE 0.009 0.001 PHE C 126 TRP 0.006 0.001 TRP D 214 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9724) covalent geometry : angle 0.68120 / 0.33 (13247) SS BOND : bond 0.00230 / 0.12 ( 2) SS BOND : angle 0.60811 / 0.25 ( 4) hydrogen bonds : bond 0.03595 / 2.43 ( 410) hydrogen bonds : angle 4.05816 / 2.89 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6517 (mt) cc_final: 0.6272 (mm) REVERT: B 162 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (pt) REVERT: B 179 MET cc_start: 0.9057 (mmm) cc_final: 0.8776 (mmm) REVERT: B 205 MET cc_start: 0.8176 (mmp) cc_final: 0.7755 (mmm) REVERT: B 212 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8355 (tt) REVERT: E 46 LYS cc_start: 0.4384 (OUTLIER) cc_final: 0.3955 (pptt) REVERT: E 52 ARG cc_start: 0.8598 (tpm170) cc_final: 0.7988 (tpm170) REVERT: E 141 MET cc_start: 0.9112 (tpp) cc_final: 0.8888 (tpt) REVERT: E 190 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8910 (mmtt) REVERT: D 144 LYS cc_start: 0.8118 (pptt) cc_final: 0.7770 (mmmt) REVERT: D 282 MET cc_start: 0.8374 (ppp) cc_final: 0.7742 (ppp) REVERT: C 214 TRP cc_start: 0.8057 (t-100) cc_final: 0.7830 (t60) REVERT: C 215 TYR cc_start: 0.8079 (t80) cc_final: 0.7858 (t80) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 0.0708 time to fit residues: 15.7058 Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 107 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN C 69 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053191 restraints weight = 53693.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054568 restraints weight = 31635.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055443 restraints weight = 21975.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056090 restraints weight = 17144.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056432 restraints weight = 14382.367| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9726 Z= 0.132 Angle : 0.691 11.236 13251 Z= 0.339 Chirality : 0.043 0.290 1621 Planarity : 0.004 0.062 1710 Dihedral : 4.420 42.240 1414 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 1.87 % Allowed : 22.31 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1315 helix: 0.61 (0.21), residues: 656 sheet: -1.42 (0.74), residues: 57 loop : -1.89 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 91 TYR 0.007 0.001 TYR C 52 PHE 0.047 0.001 PHE A 87 TRP 0.005 0.001 TRP D 214 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9724) covalent geometry : angle 0.69148 / 0.34 (13247) SS BOND : bond 0.00230 / 0.12 ( 2) SS BOND : angle 0.56570 / 0.24 ( 4) hydrogen bonds : bond 0.03580 / 2.41 ( 410) hydrogen bonds : angle 4.05482 / 2.89 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.49 seconds wall clock time: 26 minutes 59.88 seconds (1619.88 seconds total)