Starting phenix.real_space_refine on Wed Feb 12 22:51:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_25586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_25586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_25586.map" model { file = "/net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_25586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t10_25586/02_2025/7t10_25586.cif" } resolution = 2.5 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= 0.103 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} 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: {'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} 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, 'GLU:plan': 5, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 2} 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: 5.54, per 1000 atoms: 0.66 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.95 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: 2.59 Time building geometry restraints manager: 2.61 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: 3.740 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- 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 8606 Z= 0.353 Angle : 0.996 9.226 11724 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 (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: 0.62 (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 TRP 0.032 0.003 TRP B 332 HIS 0.010 0.003 HIS B 54 PHE 0.038 0.004 PHE B 151 TYR 0.028 0.004 TYR S 95 ARG 0.013 0.001 ARG S 98 *********************** 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 : 0.951 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: 1.3446 time to fit residues: 168.5381 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 : 0.929 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.170063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117403 restraints weight = 8293.880| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.76 r_work: 0.3233 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8606 Z= 0.262 Angle : 0.724 7.665 11724 Z= 0.407 Chirality : 0.047 0.167 1378 Planarity : 0.005 0.051 1474 Dihedral : 5.226 48.048 1225 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.58 % Allowed : 8.40 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.24), residues: 1126 helix: 2.56 (0.26), residues: 394 sheet: 1.29 (0.32), residues: 243 loop : -1.25 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.002 HIS B 54 PHE 0.021 0.003 PHE B 151 TYR 0.019 0.002 TYR S 95 ARG 0.004 0.001 ARG S 179 *********************** 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 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.893 Fit side-chains REVERT: A 308 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7209 (mt-10) REVERT: B 219 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7852 (mtt90) REVERT: S 19 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7553 (ttmt) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 1.2933 time to fit residues: 158.1409 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 84 ASN R 276 ASN R 308 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3996 r_free = 0.3996 target = 0.173712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121549 restraints weight = 8552.211| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.78 r_work: 0.3287 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8606 Z= 0.168 Angle : 0.570 5.930 11724 Z= 0.319 Chirality : 0.043 0.152 1378 Planarity : 0.004 0.053 1474 Dihedral : 4.734 45.974 1220 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.34 % Allowed : 9.26 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.25), residues: 1126 helix: 2.83 (0.26), residues: 394 sheet: 1.31 (0.31), residues: 265 loop : -1.33 (0.24), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.013 0.001 TYR R 211 ARG 0.003 0.000 ARG A 21 *********************** 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 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.991 Fit side-chains REVERT: A 308 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7108 (mt-10) REVERT: B 219 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7905 (mtt-85) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 1.3110 time to fit residues: 155.8675 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 103 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124569 restraints weight = 8481.370| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.77 r_work: 0.3326 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8606 Z= 0.139 Angle : 0.510 5.209 11724 Z= 0.284 Chirality : 0.041 0.141 1378 Planarity : 0.004 0.054 1474 Dihedral : 4.415 43.993 1220 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.07 % Allowed : 9.26 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.43 (0.25), residues: 1126 helix: 3.05 (0.26), residues: 394 sheet: 1.23 (0.32), residues: 269 loop : -1.22 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR R 180 ARG 0.002 0.000 ARG S 179 *********************** 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 121 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.881 Fit side-chains REVERT: A 308 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7097 (mt-10) REVERT: B 61 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (ppp) REVERT: B 219 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7897 (mtt-85) outliers start: 17 outliers final: 8 residues processed: 115 average time/residue: 1.2967 time to fit residues: 158.6555 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.176857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124130 restraints weight = 8490.793| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.76 r_work: 0.3305 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8606 Z= 0.127 Angle : 0.484 4.949 11724 Z= 0.269 Chirality : 0.041 0.140 1378 Planarity : 0.003 0.049 1474 Dihedral : 4.234 42.345 1220 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.58 % Allowed : 10.84 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.53 (0.25), residues: 1126 helix: 3.13 (0.27), residues: 395 sheet: 1.29 (0.32), residues: 267 loop : -1.15 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR S 178 ARG 0.001 0.000 ARG S 179 *********************** 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 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.925 Fit side-chains REVERT: A 308 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 61 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8360 (ppp) REVERT: B 219 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7908 (mtt-85) outliers start: 13 outliers final: 5 residues processed: 109 average time/residue: 1.2893 time to fit residues: 149.8448 Evaluate side-chains 103 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 194 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 B residue 234 PHE Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN R 102 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119975 restraints weight = 8345.709| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.74 r_work: 0.3260 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8606 Z= 0.176 Angle : 0.554 6.115 11724 Z= 0.308 Chirality : 0.043 0.147 1378 Planarity : 0.004 0.053 1474 Dihedral : 4.310 24.071 1218 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 10.84 % 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 (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: 1.56 (0.25), residues: 1126 helix: 3.17 (0.26), residues: 389 sheet: 1.28 (0.33), residues: 254 loop : -0.99 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.001 TYR S 95 ARG 0.002 0.000 ARG S 148 *********************** 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 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.903 Fit side-chains REVERT: A 308 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7166 (mt-10) REVERT: B 260 GLU cc_start: 0.8303 (tt0) cc_final: 0.8096 (tt0) REVERT: S 19 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7645 (tttt) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 1.2948 time to fit residues: 148.9840 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.171799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118488 restraints weight = 8327.849| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.74 r_work: 0.3236 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8606 Z= 0.187 Angle : 0.576 6.384 11724 Z= 0.320 Chirality : 0.043 0.147 1378 Planarity : 0.004 0.055 1474 Dihedral : 4.441 24.613 1218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 11.45 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.50 (0.25), residues: 1126 helix: 3.08 (0.26), residues: 389 sheet: 1.33 (0.33), residues: 252 loop : -1.03 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.012 0.001 TYR S 95 ARG 0.002 0.000 ARG S 179 *********************** 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 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.183 Fit side-chains REVERT: A 308 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7201 (mt-10) REVERT: B 219 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7920 (mtt-85) REVERT: B 260 GLU cc_start: 0.8288 (tt0) cc_final: 0.8068 (tt0) REVERT: B 273 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8632 (mp) REVERT: S 19 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7709 (tttt) REVERT: S 183 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8778 (tt) outliers start: 13 outliers final: 6 residues processed: 110 average time/residue: 1.2603 time to fit residues: 147.9227 Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.170476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116835 restraints weight = 8453.534| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.76 r_work: 0.3219 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8606 Z= 0.209 Angle : 0.605 6.851 11724 Z= 0.336 Chirality : 0.044 0.150 1378 Planarity : 0.004 0.056 1474 Dihedral : 4.579 25.274 1218 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.58 % Allowed : 11.45 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.42 (0.25), residues: 1126 helix: 2.98 (0.26), residues: 389 sheet: 1.40 (0.33), residues: 240 loop : -1.06 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.007 0.001 HIS S 35 PHE 0.018 0.002 PHE B 199 TYR 0.013 0.002 TYR S 95 ARG 0.002 0.000 ARG S 179 *********************** 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 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.889 Fit side-chains REVERT: B 219 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: B 260 GLU cc_start: 0.8307 (tt0) cc_final: 0.8094 (tt0) REVERT: B 273 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8650 (mp) REVERT: S 19 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7689 (ttmt) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 1.2727 time to fit residues: 143.5049 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.0050 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.174110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121402 restraints weight = 8554.774| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.78 r_work: 0.3278 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8606 Z= 0.144 Angle : 0.518 5.396 11724 Z= 0.288 Chirality : 0.041 0.139 1378 Planarity : 0.004 0.055 1474 Dihedral : 4.241 23.779 1218 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.22 % Allowed : 11.94 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.56 (0.25), residues: 1126 helix: 3.14 (0.26), residues: 389 sheet: 1.36 (0.32), residues: 265 loop : -1.08 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR R 312 ARG 0.002 0.000 ARG S 148 *********************** 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 : 1.024 Fit side-chains REVERT: B 219 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7955 (mtt-85) REVERT: S 19 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7707 (tttt) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 1.3185 time to fit residues: 151.6503 Evaluate side-chains 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.177155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124735 restraints weight = 8496.971| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.75 r_work: 0.3320 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8606 Z= 0.124 Angle : 0.482 5.155 11724 Z= 0.266 Chirality : 0.040 0.136 1378 Planarity : 0.004 0.055 1474 Dihedral : 3.995 22.344 1218 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.10 % Allowed : 12.30 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.68 (0.25), residues: 1126 helix: 3.26 (0.26), residues: 389 sheet: 1.35 (0.32), residues: 266 loop : -0.98 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 178 ARG 0.002 0.000 ARG S 148 ********************** 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 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.961 Fit side-chains REVERT: B 219 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7869 (mtt-85) REVERT: S 19 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7710 (tttt) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 1.2486 time to fit residues: 143.7185 Evaluate side-chains 104 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3985 r_free = 0.3985 target = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121115 restraints weight = 8557.114| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.75 r_work: 0.3274 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8606 Z= 0.156 Angle : 0.526 5.447 11724 Z= 0.292 Chirality : 0.042 0.142 1378 Planarity : 0.004 0.055 1474 Dihedral : 4.168 23.349 1218 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.85 % Allowed : 12.67 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.60 (0.25), residues: 1126 helix: 3.20 (0.26), residues: 389 sheet: 1.25 (0.33), residues: 255 loop : -0.94 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR S 95 ARG 0.002 0.000 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8434.84 seconds wall clock time: 148 minutes 56.83 seconds (8936.83 seconds total)