Starting phenix.real_space_refine on Fri Mar 14 07:44:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_36304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_36304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_36304.map" model { file = "/net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_36304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jia_36304/03_2025/8jia_36304.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 13} 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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 6.64, per 1000 atoms: 0.69 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.85 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: 2.27 Time building geometry restraints manager: 2.87 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 - 16.12: 5412 16.12 - 32.23: 363 32.23 - 48.35: 79 48.35 - 64.47: 24 64.47 - 80.58: 7 Dihedral angle restraints: 5885 sinusoidal: 2067 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 5882 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: 3.880 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.740 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 9724 Z= 0.298 Angle : 1.062 13.944 13247 Z= 0.546 Chirality : 0.056 0.265 1621 Planarity : 0.006 0.074 1710 Dihedral : 12.520 80.584 3403 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (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 TRP 0.006 0.001 TRP C 274 HIS 0.016 0.002 HIS B 199 PHE 0.019 0.002 PHE D 110 TYR 0.028 0.002 TYR C 255 ARG 0.010 0.001 ARG A 187 *********************** 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 : 1.126 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: 0.8682 (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: 0.2013 time to fit residues: 52.1031 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 : 1.155 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3568 r_free = 0.3568 target = 0.071466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057309 restraints weight = 52192.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058612 restraints weight = 31819.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059552 restraints weight = 22570.002| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9724 Z= 0.199 Angle : 0.618 7.465 13247 Z= 0.319 Chirality : 0.041 0.136 1621 Planarity : 0.004 0.044 1710 Dihedral : 7.882 89.969 1478 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.39 % Favored : 93.31 % Rotamer: Outliers : 1.54 % Allowed : 9.23 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.22), residues: 1315 helix: -0.39 (0.20), residues: 649 sheet: -2.57 (0.61), residues: 62 loop : -2.31 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.005 0.001 HIS E 189 PHE 0.015 0.001 PHE A 87 TYR 0.007 0.001 TYR C 288 ARG 0.008 0.000 ARG A 187 *********************** 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8749 (m-10) cc_final: 0.8427 (m-10) REVERT: A 187 ARG cc_start: 0.8479 (mtm110) cc_final: 0.7983 (mtm-85) REVERT: B 205 MET cc_start: 0.8058 (mmp) cc_final: 0.7637 (mmp) REVERT: E 52 ARG cc_start: 0.8233 (tpm170) cc_final: 0.7570 (tpp-160) REVERT: E 305 MET cc_start: 0.8482 (tmm) cc_final: 0.8137 (tmm) REVERT: D 160 ASP cc_start: 0.8468 (m-30) cc_final: 0.7976 (t0) REVERT: D 180 GLN cc_start: 0.8934 (tp40) cc_final: 0.8620 (tp-100) REVERT: D 217 GLN cc_start: 0.8845 (pm20) cc_final: 0.8628 (pm20) REVERT: D 223 GLU cc_start: 0.8619 (pm20) cc_final: 0.8324 (pm20) REVERT: D 225 MET cc_start: 0.9026 (mmm) cc_final: 0.8810 (mmp) REVERT: D 248 GLU cc_start: 0.7580 (tp30) cc_final: 0.7127 (tp30) REVERT: D 252 ASN cc_start: 0.8479 (m110) cc_final: 0.7105 (m110) REVERT: D 282 MET cc_start: 0.8489 (ppp) cc_final: 0.8018 (ppp) REVERT: C 214 TRP cc_start: 0.8172 (t-100) cc_final: 0.7901 (t60) REVERT: C 278 LEU cc_start: 0.9344 (tp) cc_final: 0.9095 (tt) outliers start: 14 outliers final: 7 residues processed: 155 average time/residue: 0.1926 time to fit residues: 43.0190 Evaluate side-chains 140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 280 VAL 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 23 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.0020 chunk 3 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.070662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056325 restraints weight = 52536.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057703 restraints weight = 31382.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058650 restraints weight = 21856.171| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9724 Z= 0.181 Angle : 0.585 10.066 13247 Z= 0.298 Chirality : 0.040 0.136 1621 Planarity : 0.003 0.045 1710 Dihedral : 7.372 88.126 1476 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 0.99 % Allowed : 14.51 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1315 helix: 0.32 (0.21), residues: 643 sheet: -2.37 (0.64), residues: 62 loop : -2.13 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.017 0.001 PHE A 87 TYR 0.013 0.001 TYR C 294 ARG 0.004 0.000 ARG A 187 *********************** 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 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.8665 (m-10) cc_final: 0.8401 (m-10) REVERT: A 90 PHE cc_start: 0.8993 (m-80) cc_final: 0.8629 (m-80) REVERT: B 205 MET cc_start: 0.8152 (mmp) cc_final: 0.7786 (mmm) REVERT: E 52 ARG cc_start: 0.8304 (tpm170) cc_final: 0.7570 (tpm170) REVERT: E 305 MET cc_start: 0.8502 (tmm) cc_final: 0.8195 (tmm) REVERT: D 160 ASP cc_start: 0.8474 (m-30) cc_final: 0.7997 (t0) REVERT: D 171 ASN cc_start: 0.8117 (p0) cc_final: 0.7764 (p0) REVERT: D 217 GLN cc_start: 0.8892 (pm20) cc_final: 0.8651 (pm20) REVERT: D 223 GLU cc_start: 0.8661 (pm20) cc_final: 0.8380 (pm20) REVERT: D 225 MET cc_start: 0.9037 (mmm) cc_final: 0.8779 (mmp) REVERT: D 248 GLU cc_start: 0.7693 (tp30) cc_final: 0.7217 (tp30) REVERT: D 252 ASN cc_start: 0.8650 (m110) cc_final: 0.7209 (m110) REVERT: C 214 TRP cc_start: 0.8179 (t-100) cc_final: 0.7848 (t60) outliers start: 9 outliers final: 7 residues processed: 151 average time/residue: 0.1943 time to fit residues: 41.8842 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 280 VAL 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 60 optimal weight: 0.0570 chunk 92 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.072242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.057326 restraints weight = 52605.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058741 restraints weight = 31830.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059679 restraints weight = 22340.658| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9724 Z= 0.149 Angle : 0.556 8.253 13247 Z= 0.281 Chirality : 0.040 0.139 1621 Planarity : 0.003 0.049 1710 Dihedral : 6.975 82.049 1476 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.93 % Favored : 93.84 % Rotamer: Outliers : 1.76 % Allowed : 16.37 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1315 helix: 0.69 (0.22), residues: 634 sheet: -2.25 (0.66), residues: 60 loop : -2.05 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 214 HIS 0.006 0.001 HIS E 189 PHE 0.010 0.001 PHE A 87 TYR 0.013 0.001 TYR C 294 ARG 0.009 0.000 ARG A 187 *********************** 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 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8519 (mmp) cc_final: 0.8296 (mmp) REVERT: B 194 MET cc_start: 0.7937 (tpp) cc_final: 0.7362 (tpp) REVERT: B 205 MET cc_start: 0.8000 (mmp) cc_final: 0.7707 (mmm) REVERT: E 52 ARG cc_start: 0.8365 (tpm170) cc_final: 0.8007 (tpm170) REVERT: E 59 GLU cc_start: 0.8363 (pp20) cc_final: 0.8140 (pp20) REVERT: E 305 MET cc_start: 0.8469 (tmm) cc_final: 0.8236 (tmm) REVERT: D 34 LEU cc_start: 0.9467 (tt) cc_final: 0.9241 (tt) REVERT: D 160 ASP cc_start: 0.8459 (m-30) cc_final: 0.7987 (t0) REVERT: D 217 GLN cc_start: 0.8820 (pm20) cc_final: 0.8613 (pm20) REVERT: D 248 GLU cc_start: 0.7689 (tp30) cc_final: 0.7190 (tp30) REVERT: D 252 ASN cc_start: 0.8628 (m110) cc_final: 0.7106 (m110) REVERT: D 282 MET cc_start: 0.8436 (ppp) cc_final: 0.8138 (ppp) REVERT: C 214 TRP cc_start: 0.8127 (t-100) cc_final: 0.7803 (t60) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 0.2143 time to fit residues: 49.0626 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 D residue 278 LEU Chi-restraints excluded: chain D residue 280 VAL 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 42 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 69 ASN E 189 HIS ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054218 restraints weight = 53504.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055554 restraints weight = 32105.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056483 restraints weight = 22519.926| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9724 Z= 0.228 Angle : 0.600 7.010 13247 Z= 0.309 Chirality : 0.041 0.162 1621 Planarity : 0.004 0.043 1710 Dihedral : 6.637 71.962 1476 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.68 % Favored : 92.09 % Rotamer: Outliers : 1.87 % Allowed : 17.14 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1315 helix: 0.49 (0.21), residues: 665 sheet: -1.82 (0.65), residues: 72 loop : -1.97 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 274 HIS 0.005 0.001 HIS C 136 PHE 0.017 0.001 PHE C 163 TYR 0.009 0.001 TYR C 265 ARG 0.005 0.001 ARG A 91 *********************** 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 152 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8831 (mmp) cc_final: 0.8561 (mmp) REVERT: B 205 MET cc_start: 0.8163 (mmp) cc_final: 0.7780 (mmm) REVERT: E 52 ARG cc_start: 0.8495 (tpm170) cc_final: 0.7885 (tpp-160) REVERT: E 67 ASP cc_start: 0.8550 (t0) cc_final: 0.8344 (t0) REVERT: D 160 ASP cc_start: 0.8503 (m-30) cc_final: 0.7997 (t0) REVERT: D 217 GLN cc_start: 0.8917 (pm20) cc_final: 0.8706 (pm20) REVERT: D 223 GLU cc_start: 0.8582 (pm20) cc_final: 0.8366 (pm20) REVERT: D 248 GLU cc_start: 0.7835 (tp30) cc_final: 0.7375 (tp30) REVERT: D 252 ASN cc_start: 0.8860 (m110) cc_final: 0.7346 (m110) REVERT: D 282 MET cc_start: 0.8420 (ppp) cc_final: 0.7837 (ppp) REVERT: C 54 ASP cc_start: 0.6642 (p0) cc_final: 0.6380 (p0) REVERT: C 214 TRP cc_start: 0.8225 (t-100) cc_final: 0.7892 (t60) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.2015 time to fit residues: 42.1062 Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU 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 17 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN C 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.069447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055587 restraints weight = 52992.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056903 restraints weight = 31083.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057954 restraints weight = 19381.770| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9724 Z= 0.179 Angle : 0.580 6.931 13247 Z= 0.295 Chirality : 0.041 0.150 1621 Planarity : 0.003 0.053 1710 Dihedral : 6.371 62.982 1476 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % Rotamer: Outliers : 1.54 % Allowed : 18.90 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1315 helix: 0.70 (0.21), residues: 651 sheet: -1.33 (0.71), residues: 61 loop : -1.88 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 306 HIS 0.002 0.001 HIS C 136 PHE 0.012 0.001 PHE C 163 TYR 0.004 0.001 TYR C 294 ARG 0.004 0.000 ARG A 187 *********************** 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 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6211 (m-10) cc_final: 0.6003 (m-10) REVERT: A 179 MET cc_start: 0.8629 (mmp) cc_final: 0.8258 (mmp) REVERT: B 205 MET cc_start: 0.8065 (mmp) cc_final: 0.7675 (mmm) REVERT: E 52 ARG cc_start: 0.8458 (tpm170) cc_final: 0.7850 (tpp-160) REVERT: E 67 ASP cc_start: 0.8404 (t0) cc_final: 0.8204 (t0) REVERT: E 141 MET cc_start: 0.9100 (tpp) cc_final: 0.8861 (tpt) REVERT: D 160 ASP cc_start: 0.8415 (m-30) cc_final: 0.7964 (t0) REVERT: D 217 GLN cc_start: 0.8891 (pm20) cc_final: 0.8674 (pm20) REVERT: D 223 GLU cc_start: 0.8595 (pm20) cc_final: 0.8321 (pm20) REVERT: D 248 GLU cc_start: 0.7750 (tp30) cc_final: 0.7305 (tp30) REVERT: D 252 ASN cc_start: 0.8851 (m110) cc_final: 0.7177 (m110) REVERT: D 282 MET cc_start: 0.8314 (ppp) cc_final: 0.7823 (ppp) REVERT: C 214 TRP cc_start: 0.8113 (t-100) cc_final: 0.7793 (t60) outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 0.1930 time to fit residues: 43.1589 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 : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS 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 31 SER 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 D residue 278 LEU 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 122 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3522 r_free = 0.3522 target = 0.069339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055050 restraints weight = 53692.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056401 restraints weight = 32407.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057364 restraints weight = 20218.870| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9724 Z= 0.191 Angle : 0.617 11.043 13247 Z= 0.311 Chirality : 0.041 0.168 1621 Planarity : 0.004 0.058 1710 Dihedral : 6.224 62.524 1476 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.84 % Favored : 92.93 % Rotamer: Outliers : 2.09 % Allowed : 20.00 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1315 helix: 0.75 (0.21), residues: 653 sheet: -1.39 (0.68), residues: 67 loop : -1.85 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 306 HIS 0.003 0.001 HIS C 136 PHE 0.012 0.001 PHE C 163 TYR 0.006 0.001 TYR C 294 ARG 0.005 0.000 ARG A 187 *********************** 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: 19 poor density : 136 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.6287 (m-10) cc_final: 0.6045 (m-10) REVERT: A 71 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6249 (mm) REVERT: A 179 MET cc_start: 0.8880 (mmp) cc_final: 0.8612 (mmp) REVERT: A 196 THR cc_start: 0.9342 (m) cc_final: 0.8979 (t) REVERT: B 162 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8699 (pt) REVERT: B 205 MET cc_start: 0.8077 (mmp) cc_final: 0.7705 (mmm) REVERT: E 46 LYS cc_start: 0.4052 (OUTLIER) cc_final: 0.3631 (pptt) REVERT: E 52 ARG cc_start: 0.8489 (tpm170) cc_final: 0.7864 (tpp-160) REVERT: E 67 ASP cc_start: 0.8489 (t0) cc_final: 0.8289 (t0) REVERT: E 141 MET cc_start: 0.9126 (tpp) cc_final: 0.8889 (tpt) REVERT: D 160 ASP cc_start: 0.8427 (m-30) cc_final: 0.7919 (t0) REVERT: D 217 GLN cc_start: 0.8890 (pm20) cc_final: 0.8679 (pm20) REVERT: D 223 GLU cc_start: 0.8596 (pm20) cc_final: 0.8304 (pm20) REVERT: D 248 GLU cc_start: 0.7792 (tp30) cc_final: 0.7411 (tp30) REVERT: D 252 ASN cc_start: 0.8856 (m110) cc_final: 0.7184 (m-40) REVERT: D 282 MET cc_start: 0.8324 (ppp) cc_final: 0.7989 (ppp) REVERT: C 54 ASP cc_start: 0.6554 (p0) cc_final: 0.6270 (p0) REVERT: C 214 TRP cc_start: 0.8138 (t-100) cc_final: 0.7814 (t60) REVERT: C 215 TYR cc_start: 0.8109 (t80) cc_final: 0.7839 (t80) REVERT: C 226 LEU cc_start: 0.9403 (mm) cc_final: 0.9164 (mm) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.1899 time to fit residues: 41.6272 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 31 SER 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 D residue 278 LEU Chi-restraints excluded: chain C residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN E 188 GLN D 17 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051962 restraints weight = 54298.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053104 restraints weight = 31760.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054168 restraints weight = 19864.218| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9724 Z= 0.308 Angle : 0.703 8.342 13247 Z= 0.362 Chirality : 0.044 0.210 1621 Planarity : 0.004 0.057 1710 Dihedral : 6.648 62.831 1476 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.83 % Favored : 91.94 % Rotamer: Outliers : 2.42 % Allowed : 19.45 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1315 helix: 0.50 (0.21), residues: 662 sheet: -1.39 (0.67), residues: 70 loop : -1.85 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 274 HIS 0.005 0.001 HIS C 136 PHE 0.026 0.002 PHE C 163 TYR 0.010 0.002 TYR C 288 ARG 0.010 0.001 ARG D 15 *********************** 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 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 THR cc_start: 0.9254 (m) cc_final: 0.8920 (t) REVERT: B 162 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (pt) REVERT: B 205 MET cc_start: 0.8380 (mmp) cc_final: 0.7988 (mmm) REVERT: D 217 GLN cc_start: 0.9009 (pm20) cc_final: 0.8726 (pm20) REVERT: D 248 GLU cc_start: 0.7751 (tp30) cc_final: 0.7507 (tp30) REVERT: C 215 TYR cc_start: 0.8138 (t80) cc_final: 0.7855 (t80) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.1886 time to fit residues: 39.9799 Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 83 ILE 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 E residue 46 LYS Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 31 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3488 r_free = 0.3488 target = 0.067857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053209 restraints weight = 53446.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054539 restraints weight = 31770.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055458 restraints weight = 22183.368| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9724 Z= 0.193 Angle : 0.654 10.296 13247 Z= 0.325 Chirality : 0.042 0.157 1621 Planarity : 0.004 0.064 1710 Dihedral : 6.365 61.262 1476 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.84 % Favored : 92.93 % Rotamer: Outliers : 1.76 % Allowed : 21.32 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1315 helix: 0.54 (0.21), residues: 668 sheet: -1.39 (0.68), residues: 70 loop : -1.84 (0.28), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 214 HIS 0.002 0.001 HIS C 136 PHE 0.013 0.001 PHE C 163 TYR 0.004 0.001 TYR E 111 ARG 0.005 0.000 ARG A 187 *********************** 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 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 THR cc_start: 0.9138 (m) cc_final: 0.8528 (p) REVERT: B 179 MET cc_start: 0.9144 (mmm) cc_final: 0.8828 (mmm) REVERT: B 205 MET cc_start: 0.8183 (mmp) cc_final: 0.7806 (mmm) REVERT: B 212 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 46 LYS cc_start: 0.4362 (OUTLIER) cc_final: 0.3897 (pptt) REVERT: E 52 ARG cc_start: 0.8564 (tpm170) cc_final: 0.7973 (tpp-160) REVERT: E 141 MET cc_start: 0.9112 (tpp) cc_final: 0.8879 (tpt) REVERT: E 352 TYR cc_start: 0.7239 (m-80) cc_final: 0.6961 (m-80) REVERT: D 144 LYS cc_start: 0.8194 (pptt) cc_final: 0.7663 (mmmt) REVERT: D 217 GLN cc_start: 0.8888 (pm20) cc_final: 0.8669 (pm20) REVERT: D 282 MET cc_start: 0.8444 (ppp) cc_final: 0.7794 (ppp) REVERT: C 215 TYR cc_start: 0.8176 (t80) cc_final: 0.7948 (t80) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.1926 time to fit residues: 42.3689 Evaluate side-chains 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL 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 212 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 31 SER 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 194 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053440 restraints weight = 54060.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054808 restraints weight = 32095.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055699 restraints weight = 22294.476| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9724 Z= 0.202 Angle : 0.665 10.867 13247 Z= 0.331 Chirality : 0.042 0.224 1621 Planarity : 0.004 0.059 1710 Dihedral : 6.275 60.805 1476 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.38 % Favored : 92.40 % Rotamer: Outliers : 1.87 % Allowed : 21.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1315 helix: 0.64 (0.21), residues: 660 sheet: -1.34 (0.68), residues: 70 loop : -1.86 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 214 HIS 0.002 0.001 HIS C 136 PHE 0.017 0.001 PHE B 46 TYR 0.005 0.001 TYR C 255 ARG 0.006 0.000 ARG A 187 ********************** 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: 17 poor density : 135 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6361 (mt) cc_final: 0.6125 (mm) REVERT: A 92 LEU cc_start: 0.9003 (mm) cc_final: 0.8787 (mm) REVERT: A 196 THR cc_start: 0.9090 (m) cc_final: 0.8572 (t) REVERT: B 179 MET cc_start: 0.9097 (mmm) cc_final: 0.8788 (mmm) REVERT: B 194 MET cc_start: 0.7872 (tpp) cc_final: 0.7419 (tpp) REVERT: B 205 MET cc_start: 0.8159 (mmp) cc_final: 0.7771 (mmm) REVERT: B 212 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8390 (tt) REVERT: E 46 LYS cc_start: 0.4414 (OUTLIER) cc_final: 0.3903 (pptt) REVERT: E 48 ASN cc_start: 0.8814 (t0) cc_final: 0.8394 (p0) REVERT: E 52 ARG cc_start: 0.8552 (tpm170) cc_final: 0.7926 (tpp-160) REVERT: E 141 MET cc_start: 0.9080 (tpp) cc_final: 0.8872 (tpt) REVERT: D 144 LYS cc_start: 0.8189 (pptt) cc_final: 0.7645 (mmmt) REVERT: D 217 GLN cc_start: 0.8871 (pm20) cc_final: 0.8654 (pm20) REVERT: D 282 MET cc_start: 0.8404 (ppp) cc_final: 0.8027 (ppp) REVERT: C 214 TRP cc_start: 0.8109 (t-100) cc_final: 0.7841 (t60) REVERT: C 215 TYR cc_start: 0.8092 (t80) cc_final: 0.7859 (t80) outliers start: 17 outliers final: 13 residues processed: 150 average time/residue: 0.1954 time to fit residues: 42.3916 Evaluate side-chains 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL 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 212 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain D residue 31 SER 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 194 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053442 restraints weight = 53164.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054753 restraints weight = 31513.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055681 restraints weight = 21978.080| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9724 Z= 0.191 Angle : 0.653 9.562 13247 Z= 0.324 Chirality : 0.042 0.206 1621 Planarity : 0.004 0.059 1710 Dihedral : 6.225 60.785 1476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.62 % Favored : 93.16 % Rotamer: Outliers : 1.65 % Allowed : 21.65 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1315 helix: 0.68 (0.21), residues: 663 sheet: -1.25 (0.68), residues: 70 loop : -1.85 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 214 HIS 0.002 0.001 HIS A 67 PHE 0.012 0.001 PHE A 154 TYR 0.004 0.001 TYR C 255 ARG 0.005 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3141.37 seconds wall clock time: 55 minutes 19.46 seconds (3319.46 seconds total)