Starting phenix.real_space_refine on Tue Mar 3 19:54:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t10_25586/03_2026/7t10_25586.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5415 2.51 5 N 1426 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8429 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2097 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1627 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 11, 'ASP:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2510 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 365 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "P" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "S" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1711 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8429 At special positions: 0 Unit cell: (89.4705, 126.111, 128.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1526 8.00 N 1426 7.00 C 5415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS P 3 " - pdb=" SG CYS P 14 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 216.9 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'R' and resid 40 through 70 removed outlier: 4.044A pdb=" N ALA R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL R 45 " --> pdb=" O THR R 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG R 70 " --> pdb=" O TYR R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 93 removed outlier: 3.680A pdb=" N ASN R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU R 85 " --> pdb=" O TYR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 removed outlier: 4.025A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 105 " --> pdb=" O MET R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 removed outlier: 3.534A pdb=" N VAL R 144 " --> pdb=" O ARG R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 152 removed outlier: 4.016A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.698A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.517A pdb=" N MET R 178 " --> pdb=" O ILE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 201 removed outlier: 3.528A pdb=" N GLU R 200 " --> pdb=" O TRP R 197 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER R 201 " --> pdb=" O PRO R 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 197 through 201' Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.728A pdb=" N TYR R 211 " --> pdb=" O GLY R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 238 Processing helix chain 'R' and resid 244 through 282 removed outlier: 3.695A pdb=" N ASN R 250 " --> pdb=" O GLU R 246 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL R 262 " --> pdb=" O VAL R 258 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 301 removed outlier: 3.645A pdb=" N THR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 313 removed outlier: 3.679A pdb=" N CYS R 306 " --> pdb=" O TYR R 302 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 319 through 327 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.998A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.228A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.656A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.107A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.956A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.501A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.590A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.556A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.901A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.622A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.975A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.401A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.955A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.051A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.872A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.987A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.601A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.868A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 6 through 7 removed outlier: 3.503A pdb=" N PHE P 7 " --> pdb=" O THR P 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.919A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.642A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.93 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: 2642 1.34 - 1.47: 2134 1.47 - 1.59: 3743 1.59 - 1.71: 0 1.71 - 1.84: 87 Bond restraints: 8606 Sorted by residual: bond pdb=" N ALA S 49 " pdb=" CA ALA S 49 " ideal model delta sigma weight residual 1.455 1.475 -0.020 1.27e-02 6.20e+03 2.56e+00 bond pdb=" N HIS B 142 " pdb=" CA HIS B 142 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.25e-02 6.40e+03 2.35e+00 bond pdb=" N TRP B 63 " pdb=" CA TRP B 63 " ideal model delta sigma weight residual 1.455 1.474 -0.019 1.30e-02 5.92e+03 2.09e+00 bond pdb=" C ALA S 49 " pdb=" N TYR S 50 " ideal model delta sigma weight residual 1.331 1.351 -0.019 1.38e-02 5.25e+03 1.99e+00 bond pdb=" CA HIS B 62 " pdb=" C HIS B 62 " ideal model delta sigma weight residual 1.520 1.537 -0.017 1.20e-02 6.94e+03 1.96e+00 ... (remaining 8601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 10929 1.85 - 3.69: 660 3.69 - 5.54: 103 5.54 - 7.38: 24 7.38 - 9.23: 8 Bond angle restraints: 11724 Sorted by residual: angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 112.77 119.47 -6.70 1.28e+00 6.10e-01 2.74e+01 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 113.75 119.66 -5.91 1.49e+00 4.50e-01 1.57e+01 angle pdb=" N GLU A 276 " pdb=" CA GLU A 276 " pdb=" CB GLU A 276 " ideal model delta sigma weight residual 110.01 115.68 -5.67 1.45e+00 4.76e-01 1.53e+01 angle pdb=" N THR B 86 " pdb=" CA THR B 86 " pdb=" C THR B 86 " ideal model delta sigma weight residual 109.59 103.34 6.25 1.61e+00 3.86e-01 1.51e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 112.88 117.77 -4.89 1.29e+00 6.01e-01 1.44e+01 ... (remaining 11719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4731 17.39 - 34.79: 195 34.79 - 52.18: 57 52.18 - 69.58: 22 69.58 - 86.97: 9 Dihedral angle restraints: 5014 sinusoidal: 1694 harmonic: 3320 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 0.00 18.26 -18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ALA C 39 " pdb=" C ALA C 39 " pdb=" N TYR C 40 " pdb=" CA TYR C 40 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual 93.00 63.79 29.21 1 1.00e+01 1.00e-02 1.22e+01 ... (remaining 5011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 845 0.045 - 0.091: 390 0.091 - 0.136: 110 0.136 - 0.181: 28 0.181 - 0.227: 5 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB VAL B 276 " pdb=" CA VAL B 276 " pdb=" CG1 VAL B 276 " pdb=" CG2 VAL B 276 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA PRO S 41 " pdb=" N PRO S 41 " pdb=" C PRO S 41 " pdb=" CB PRO S 41 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1375 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 272 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP A 272 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 272 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 273 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO S 14 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 298 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ASP B 298 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 298 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 299 " -0.014 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1263 2.77 - 3.30: 7465 3.30 - 3.83: 12749 3.83 - 4.37: 15025 4.37 - 4.90: 27152 Nonbonded interactions: 63654 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.235 3.040 nonbonded pdb=" O GLY S 9 " pdb=" NH1 ARG S 18 " model vdw 2.238 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.253 3.040 nonbonded pdb=" NE2 GLN R 102 " pdb=" OG SER R 192 " model vdw 2.277 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.307 3.040 ... (remaining 63649 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.054 8609 Z= 0.288 Angle : 0.997 9.226 11730 Z= 0.579 Chirality : 0.056 0.227 1378 Planarity : 0.006 0.062 1474 Dihedral : 12.364 86.973 2863 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.73 % Allowed : 8.04 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1126 helix: 1.80 (0.26), residues: 387 sheet: 1.35 (0.32), residues: 238 loop : -1.24 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 98 TYR 0.028 0.004 TYR S 95 PHE 0.038 0.004 PHE B 151 TRP 0.032 0.003 TRP B 332 HIS 0.010 0.003 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8606) covalent geometry : angle 0.99629 (11724) SS BOND : bond 0.01091 ( 3) SS BOND : angle 2.36641 ( 6) hydrogen bonds : bond 0.16517 ( 430) hydrogen bonds : angle 5.63356 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.244 Fit side-chains REVERT: R 252 ARG cc_start: 0.6363 (mtm110) cc_final: 0.6054 (mtm180) REVERT: A 35 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7819 (mptt) REVERT: B 262 MET cc_start: 0.8406 (ttm) cc_final: 0.8148 (ttm) outliers start: 6 outliers final: 4 residues processed: 118 average time/residue: 0.5970 time to fit residues: 74.6781 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain P residue 11 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 125 ASN R 304 ASN R 308 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS S 171 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.174474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122713 restraints weight = 8519.608| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.77 r_work: 0.3302 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8609 Z= 0.158 Angle : 0.615 5.939 11730 Z= 0.346 Chirality : 0.044 0.165 1378 Planarity : 0.004 0.047 1474 Dihedral : 4.906 46.364 1225 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.22 % Allowed : 8.53 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1126 helix: 2.76 (0.26), residues: 394 sheet: 1.36 (0.31), residues: 272 loop : -1.27 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 21 TYR 0.016 0.002 TYR R 180 PHE 0.018 0.002 PHE B 199 TRP 0.015 0.002 TRP B 332 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8606) covalent geometry : angle 0.61435 (11724) SS BOND : bond 0.00689 ( 3) SS BOND : angle 1.31805 ( 6) hydrogen bonds : bond 0.06786 ( 430) hydrogen bonds : angle 4.31528 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.260 Fit side-chains REVERT: B 219 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: S 113 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7407 (mp10) outliers start: 10 outliers final: 4 residues processed: 119 average time/residue: 0.5770 time to fit residues: 72.9450 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 79 ASN R 276 ASN R 308 ASN A 22 ASN B 340 ASN S 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118129 restraints weight = 8390.788| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.77 r_work: 0.3245 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8609 Z= 0.185 Angle : 0.651 6.995 11730 Z= 0.364 Chirality : 0.045 0.158 1378 Planarity : 0.005 0.055 1474 Dihedral : 4.964 47.220 1220 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.83 % Allowed : 9.38 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1126 helix: 2.77 (0.26), residues: 393 sheet: 1.24 (0.32), residues: 243 loop : -1.23 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 21 TYR 0.016 0.002 TYR S 95 PHE 0.020 0.002 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8606) covalent geometry : angle 0.65052 (11724) SS BOND : bond 0.00929 ( 3) SS BOND : angle 1.65191 ( 6) hydrogen bonds : bond 0.07430 ( 430) hydrogen bonds : angle 4.24172 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.226 Fit side-chains REVERT: B 61 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8341 (ppp) REVERT: B 219 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7607 (mtm180) outliers start: 15 outliers final: 8 residues processed: 115 average time/residue: 0.5795 time to fit residues: 70.7292 Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN R 308 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114010 restraints weight = 8424.853| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.12 r_work: 0.3145 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8609 Z= 0.208 Angle : 0.696 7.964 11730 Z= 0.387 Chirality : 0.047 0.163 1378 Planarity : 0.005 0.059 1474 Dihedral : 5.130 48.172 1220 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.19 % Allowed : 9.62 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1126 helix: 2.72 (0.26), residues: 388 sheet: 1.18 (0.34), residues: 238 loop : -1.15 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 179 TYR 0.017 0.002 TYR R 211 PHE 0.021 0.002 PHE B 151 TRP 0.016 0.002 TRP B 63 HIS 0.006 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8606) covalent geometry : angle 0.69530 (11724) SS BOND : bond 0.01002 ( 3) SS BOND : angle 1.81626 ( 6) hydrogen bonds : bond 0.08065 ( 430) hydrogen bonds : angle 4.27335 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.330 Fit side-chains REVERT: B 217 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8333 (pmt) REVERT: B 219 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7850 (mtt90) REVERT: B 273 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8696 (mp) REVERT: S 19 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7581 (ttmt) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.6038 time to fit residues: 70.3648 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117105 restraints weight = 8431.304| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.80 r_work: 0.3223 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8609 Z= 0.159 Angle : 0.598 6.846 11730 Z= 0.333 Chirality : 0.043 0.148 1378 Planarity : 0.004 0.058 1474 Dihedral : 4.851 47.032 1220 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.07 % Allowed : 10.72 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1126 helix: 2.87 (0.26), residues: 388 sheet: 1.14 (0.33), residues: 258 loop : -1.16 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.013 0.001 TYR R 211 PHE 0.018 0.002 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8606) covalent geometry : angle 0.59754 (11724) SS BOND : bond 0.00845 ( 3) SS BOND : angle 1.45035 ( 6) hydrogen bonds : bond 0.06684 ( 430) hydrogen bonds : angle 4.04273 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.289 Fit side-chains REVERT: B 219 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7926 (mtt-85) REVERT: S 19 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7435 (tppt) REVERT: S 183 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8771 (tt) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.5934 time to fit residues: 71.1216 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.0050 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN S 171 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120982 restraints weight = 8424.572| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.76 r_work: 0.3270 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8609 Z= 0.126 Angle : 0.528 5.630 11730 Z= 0.294 Chirality : 0.042 0.139 1378 Planarity : 0.004 0.057 1474 Dihedral : 4.551 45.330 1220 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.19 % Allowed : 10.48 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1126 helix: 3.06 (0.26), residues: 388 sheet: 1.24 (0.32), residues: 269 loop : -1.15 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.010 0.001 TYR R 180 PHE 0.016 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8606) covalent geometry : angle 0.52723 (11724) SS BOND : bond 0.00682 ( 3) SS BOND : angle 1.11372 ( 6) hydrogen bonds : bond 0.05569 ( 430) hydrogen bonds : angle 3.84396 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.332 Fit side-chains REVERT: B 61 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8131 (pp-130) REVERT: S 19 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7458 (tppt) outliers start: 18 outliers final: 7 residues processed: 116 average time/residue: 0.5939 time to fit residues: 73.1512 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 59 optimal weight: 0.0020 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN S 171 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128173 restraints weight = 8651.956| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.77 r_work: 0.3370 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8609 Z= 0.094 Angle : 0.461 4.960 11730 Z= 0.254 Chirality : 0.040 0.149 1378 Planarity : 0.003 0.052 1474 Dihedral : 4.087 41.820 1220 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.58 % Allowed : 11.33 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1126 helix: 3.09 (0.26), residues: 395 sheet: 1.29 (0.32), residues: 268 loop : -1.07 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 148 TYR 0.013 0.001 TYR S 178 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP R 269 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 8606) covalent geometry : angle 0.46076 (11724) SS BOND : bond 0.00448 ( 3) SS BOND : angle 0.66150 ( 6) hydrogen bonds : bond 0.03969 ( 430) hydrogen bonds : angle 3.61586 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.313 Fit side-chains REVERT: S 19 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7691 (tttt) outliers start: 13 outliers final: 3 residues processed: 113 average time/residue: 0.5607 time to fit residues: 67.4641 Evaluate side-chains 101 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117163 restraints weight = 8314.620| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.73 r_work: 0.3224 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8609 Z= 0.166 Angle : 0.606 6.997 11730 Z= 0.335 Chirality : 0.044 0.149 1378 Planarity : 0.004 0.057 1474 Dihedral : 4.472 24.500 1218 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.97 % Allowed : 13.03 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1126 helix: 3.01 (0.26), residues: 389 sheet: 1.48 (0.34), residues: 237 loop : -1.03 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 179 TYR 0.014 0.002 TYR S 95 PHE 0.017 0.002 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.008 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8606) covalent geometry : angle 0.60507 (11724) SS BOND : bond 0.00882 ( 3) SS BOND : angle 1.40471 ( 6) hydrogen bonds : bond 0.06576 ( 430) hydrogen bonds : angle 3.99558 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.311 Fit side-chains REVERT: R 178 MET cc_start: 0.7402 (ttp) cc_final: 0.6908 (ptm) REVERT: S 19 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7525 (tppt) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.5764 time to fit residues: 67.3181 Evaluate side-chains 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117450 restraints weight = 8386.846| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.75 r_work: 0.3223 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8609 Z= 0.158 Angle : 0.594 6.664 11730 Z= 0.328 Chirality : 0.043 0.146 1378 Planarity : 0.004 0.056 1474 Dihedral : 4.501 24.376 1218 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.22 % Allowed : 12.91 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1126 helix: 2.92 (0.26), residues: 389 sheet: 1.36 (0.33), residues: 250 loop : -1.13 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 148 TYR 0.013 0.002 TYR S 95 PHE 0.018 0.002 PHE B 199 TRP 0.013 0.001 TRP B 63 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8606) covalent geometry : angle 0.59295 (11724) SS BOND : bond 0.00871 ( 3) SS BOND : angle 1.38586 ( 6) hydrogen bonds : bond 0.06477 ( 430) hydrogen bonds : angle 3.99646 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.357 Fit side-chains REVERT: R 178 MET cc_start: 0.7384 (ttp) cc_final: 0.6897 (ptm) REVERT: S 19 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7518 (tppt) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.6111 time to fit residues: 69.8867 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.171274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117752 restraints weight = 8377.466| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.74 r_work: 0.3231 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8609 Z= 0.151 Angle : 0.582 6.434 11730 Z= 0.322 Chirality : 0.043 0.145 1378 Planarity : 0.004 0.056 1474 Dihedral : 4.476 24.370 1218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.10 % Allowed : 12.91 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.25), residues: 1126 helix: 2.91 (0.26), residues: 389 sheet: 1.25 (0.33), residues: 256 loop : -1.10 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 179 TYR 0.013 0.001 TYR S 95 PHE 0.017 0.002 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8606) covalent geometry : angle 0.58143 (11724) SS BOND : bond 0.00840 ( 3) SS BOND : angle 1.33264 ( 6) hydrogen bonds : bond 0.06327 ( 430) hydrogen bonds : angle 3.98529 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.345 Fit side-chains REVERT: R 178 MET cc_start: 0.7341 (ttp) cc_final: 0.6856 (ptm) REVERT: S 19 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7511 (tppt) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.6052 time to fit residues: 67.8438 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.171572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118043 restraints weight = 8361.748| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.75 r_work: 0.3236 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8609 Z= 0.147 Angle : 0.574 6.280 11730 Z= 0.318 Chirality : 0.043 0.144 1378 Planarity : 0.004 0.056 1474 Dihedral : 4.444 24.244 1218 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 12.79 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1126 helix: 2.94 (0.26), residues: 389 sheet: 1.31 (0.33), residues: 252 loop : -1.13 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 179 TYR 0.013 0.001 TYR S 95 PHE 0.017 0.002 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8606) covalent geometry : angle 0.57382 (11724) SS BOND : bond 0.00838 ( 3) SS BOND : angle 1.31758 ( 6) hydrogen bonds : bond 0.06194 ( 430) hydrogen bonds : angle 3.95782 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.19 seconds wall clock time: 71 minutes 40.45 seconds (4300.45 seconds total)