Starting phenix.real_space_refine on Thu Jul 2 11:49:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.cif" model { file = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2026/7scg_25034.cif" } resolution = 3.0 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= 1.000 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 64 5.16 5 C 5460 2.51 5 N 1454 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2158 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'8RI': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.82, per 1000 atoms: 0.21 Number of scatterers: 8539 At special positions: 0 Unit cell: (103.244, 122.332, 111.92, 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 64 16.00 O 1561 8.00 N 1454 7.00 C 5460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 0.70 Conformation dependent library (CDL) restraints added in 438.5 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 67 through 97 removed outlier: 4.002A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.691A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 171 removed outlier: 3.845A pdb=" N CYS D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.734A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 205 removed outlier: 3.621A pdb=" N TRP D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.653A pdb=" N VAL D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 261 No H-bonds generated for 'chain 'D' and resid 260 through 261' Processing helix chain 'D' and resid 262 through 266 removed outlier: 3.855A pdb=" N SER D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 304 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.517A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 323 " --> pdb=" O HIS D 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.937A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.773A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.533A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.958A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.196A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.733A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.755A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.635A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.692A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.763A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 206 through 210 removed outlier: 3.724A pdb=" N THR D 218 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 209 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 216 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.913A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.379A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 142 through 147 removed outlier: 3.618A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1128 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: 1.32 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1351 1.31 - 1.44: 2431 1.44 - 1.56: 4842 1.56 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8716 Sorted by residual: bond pdb=" C01 8RI D 401 " pdb=" N01 8RI D 401 " ideal model delta sigma weight residual 1.341 1.469 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C03 8RI D 401 " pdb=" C04 8RI D 401 " ideal model delta sigma weight residual 1.464 1.568 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C01 8RI D 401 " pdb=" C02 8RI D 401 " ideal model delta sigma weight residual 1.485 1.547 -0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C22 8RI D 401 " pdb=" O02 8RI D 401 " ideal model delta sigma weight residual 1.350 1.400 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.32e-02 5.74e+03 5.42e+00 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11562 1.63 - 3.25: 224 3.25 - 4.88: 43 4.88 - 6.50: 9 6.50 - 8.13: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" C ASN D 150 " pdb=" CA ASN D 150 " pdb=" CB ASN D 150 " ideal model delta sigma weight residual 110.37 117.34 -6.97 1.78e+00 3.16e-01 1.53e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 114.17 109.91 4.26 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N ASN D 150 " pdb=" CA ASN D 150 " pdb=" C ASN D 150 " ideal model delta sigma weight residual 113.02 109.14 3.88 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.20 109.72 3.48 1.21e+00 6.83e-01 8.27e+00 angle pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4678 17.70 - 35.40: 394 35.40 - 53.11: 50 53.11 - 70.81: 5 70.81 - 88.51: 4 Dihedral angle restraints: 5131 sinusoidal: 1875 harmonic: 3256 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1078 0.049 - 0.098: 239 0.098 - 0.147: 59 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA ASN D 150 " pdb=" N ASN D 150 " pdb=" C ASN D 150 " pdb=" CB ASN D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA MET D 151 " pdb=" N MET D 151 " pdb=" C MET D 151 " pdb=" CB MET D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1376 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 149 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C TYR D 149 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR D 149 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN D 150 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR B 164 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 164 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 200 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 201 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " 0.022 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2214 2.80 - 3.32: 7517 3.32 - 3.85: 12922 3.85 - 4.37: 15157 4.37 - 4.90: 28551 Nonbonded interactions: 66361 Sorted by model distance: nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.274 3.120 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.280 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR D 101 " pdb=" OD1 ASN D 104 " model vdw 2.304 3.040 ... (remaining 66356 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: 1.080 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.040 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 0.128 8719 Z= 0.224 Angle : 0.610 8.129 11848 Z= 0.340 Chirality : 0.043 0.245 1379 Planarity : 0.004 0.038 1486 Dihedral : 12.826 88.509 3020 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.30 (0.26), residues: 1105 helix: 1.82 (0.28), residues: 371 sheet: -0.93 (0.31), residues: 294 loop : -1.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.011 0.002 TYR E 50 PHE 0.013 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 ( 8716) covalent geometry : angle 0.60956 / 0.34 (11842) SS BOND : bond 0.00625 / 0.31 ( 3) SS BOND : angle 0.67504 / 0.33 ( 6) hydrogen bonds : bond 0.17825 / 12.51 ( 398) hydrogen bonds : angle 6.36831 / 4.52 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.371 Fit side-chains REVERT: B 247 ASP cc_start: 0.7577 (t0) cc_final: 0.7377 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.6275 time to fit residues: 77.1403 Evaluate side-chains 100 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100206 restraints weight = 11009.153| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.31 r_work: 0.3166 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8719 Z= 0.105 Angle : 0.543 7.612 11848 Z= 0.283 Chirality : 0.042 0.149 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.486 36.156 1214 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.01 % Allowed : 7.66 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.14 (0.26), residues: 1105 helix: 2.13 (0.28), residues: 371 sheet: -0.52 (0.30), residues: 296 loop : -1.25 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.019 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 8716) covalent geometry : angle 0.54257 / 0.28 (11842) SS BOND : bond 0.00544 / 0.26 ( 3) SS BOND : angle 0.60325 / 0.33 ( 6) hydrogen bonds : bond 0.04292 / 2.81 ( 398) hydrogen bonds : angle 4.38095 / 3.06 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.342 Fit side-chains REVERT: D 243 MET cc_start: 0.7750 (ttp) cc_final: 0.7537 (ttt) REVERT: A 205 ARG cc_start: 0.7866 (pmt170) cc_final: 0.7474 (mmm160) outliers start: 9 outliers final: 2 residues processed: 125 average time/residue: 0.6089 time to fit residues: 80.7350 Evaluate side-chains 109 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 52 optimal weight: 0.0000 chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 17 GLN B 75 GLN D 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095518 restraints weight = 10933.132| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.30 r_work: 0.3089 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8719 Z= 0.168 Angle : 0.595 8.225 11848 Z= 0.307 Chirality : 0.043 0.151 1379 Planarity : 0.004 0.035 1486 Dihedral : 4.621 41.746 1214 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.25 % Allowed : 10.14 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.32 (0.26), residues: 1105 helix: 2.24 (0.28), residues: 371 sheet: -0.27 (0.31), residues: 288 loop : -1.21 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8716) covalent geometry : angle 0.59482 / 0.31 (11842) SS BOND : bond 0.00646 / 0.31 ( 3) SS BOND : angle 0.63526 / 0.37 ( 6) hydrogen bonds : bond 0.05033 / 3.30 ( 398) hydrogen bonds : angle 4.32096 / 3.02 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.328 Fit side-chains REVERT: A 205 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7656 (mmm160) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.6226 time to fit residues: 74.6009 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098590 restraints weight = 11133.181| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.32 r_work: 0.3151 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8719 Z= 0.129 Angle : 0.547 7.015 11848 Z= 0.285 Chirality : 0.042 0.149 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.454 42.956 1214 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.36 % Allowed : 12.61 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.47 (0.26), residues: 1105 helix: 2.37 (0.28), residues: 371 sheet: -0.19 (0.31), residues: 290 loop : -1.12 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8716) covalent geometry : angle 0.54733 / 0.28 (11842) SS BOND : bond 0.00519 / 0.25 ( 3) SS BOND : angle 0.67390 / 0.39 ( 6) hydrogen bonds : bond 0.04408 / 2.88 ( 398) hydrogen bonds : angle 4.12710 / 2.88 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.294 Fit side-chains REVERT: A 205 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7677 (mmm160) outliers start: 21 outliers final: 10 residues processed: 117 average time/residue: 0.6127 time to fit residues: 76.0578 Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091421 restraints weight = 10820.607| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.30 r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8719 Z= 0.215 Angle : 0.639 9.339 11848 Z= 0.327 Chirality : 0.045 0.153 1379 Planarity : 0.004 0.037 1486 Dihedral : 4.820 45.948 1214 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.15 % Allowed : 13.74 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.39 (0.26), residues: 1105 helix: 2.29 (0.27), residues: 371 sheet: -0.21 (0.30), residues: 290 loop : -1.18 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 98 TYR 0.016 0.002 TYR B 105 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 8716) covalent geometry : angle 0.63876 / 0.33 (11842) SS BOND : bond 0.00680 / 0.33 ( 3) SS BOND : angle 0.75062 / 0.43 ( 6) hydrogen bonds : bond 0.05424 / 3.55 ( 398) hydrogen bonds : angle 4.28420 / 2.99 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.359 Fit side-chains REVERT: B 247 ASP cc_start: 0.7835 (t0) cc_final: 0.7628 (t0) REVERT: B 327 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 309 ASP cc_start: 0.8129 (p0) cc_final: 0.7891 (p0) outliers start: 28 outliers final: 15 residues processed: 122 average time/residue: 0.6149 time to fit residues: 79.6233 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095359 restraints weight = 10774.448| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.29 r_work: 0.3162 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8719 Z= 0.112 Angle : 0.524 7.390 11848 Z= 0.273 Chirality : 0.041 0.150 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.399 45.146 1214 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.14 % Allowed : 14.75 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.66 (0.26), residues: 1105 helix: 2.48 (0.28), residues: 372 sheet: 0.05 (0.31), residues: 278 loop : -1.06 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8716) covalent geometry : angle 0.52368 / 0.27 (11842) SS BOND : bond 0.00494 / 0.24 ( 3) SS BOND : angle 0.69913 / 0.40 ( 6) hydrogen bonds : bond 0.04116 / 2.68 ( 398) hydrogen bonds : angle 4.01911 / 2.80 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.404 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.5646 time to fit residues: 75.8019 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093454 restraints weight = 10875.592| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.30 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8719 Z= 0.152 Angle : 0.567 8.209 11848 Z= 0.293 Chirality : 0.043 0.150 1379 Planarity : 0.003 0.035 1486 Dihedral : 4.536 45.567 1214 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.82 % Allowed : 15.09 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.65 (0.26), residues: 1105 helix: 2.45 (0.27), residues: 375 sheet: 0.06 (0.31), residues: 280 loop : -1.09 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.014 0.001 TYR E 178 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 8716) covalent geometry : angle 0.56663 / 0.29 (11842) SS BOND : bond 0.00564 / 0.27 ( 3) SS BOND : angle 0.66294 / 0.38 ( 6) hydrogen bonds : bond 0.04649 / 3.03 ( 398) hydrogen bonds : angle 4.08497 / 2.86 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.271 Fit side-chains REVERT: B 247 ASP cc_start: 0.7871 (t0) cc_final: 0.7610 (t0) REVERT: B 327 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8651 (t) REVERT: E 51 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8420 (tp) outliers start: 25 outliers final: 16 residues processed: 125 average time/residue: 0.4979 time to fit residues: 66.3654 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097993 restraints weight = 10984.086| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.31 r_work: 0.3135 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8719 Z= 0.138 Angle : 0.551 7.816 11848 Z= 0.286 Chirality : 0.042 0.151 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.469 45.301 1214 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.48 % Allowed : 16.10 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.69 (0.26), residues: 1105 helix: 2.61 (0.27), residues: 369 sheet: 0.01 (0.30), residues: 292 loop : -1.12 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.015 0.001 TYR E 178 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8716) covalent geometry : angle 0.55127 / 0.29 (11842) SS BOND : bond 0.00548 / 0.26 ( 3) SS BOND : angle 0.60375 / 0.34 ( 6) hydrogen bonds : bond 0.04431 / 2.89 ( 398) hydrogen bonds : angle 4.02719 / 2.81 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.310 Fit side-chains REVERT: B 247 ASP cc_start: 0.7816 (t0) cc_final: 0.7537 (t0) REVERT: B 262 MET cc_start: 0.9249 (tpp) cc_final: 0.9025 (ttm) REVERT: B 327 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8644 (t) REVERT: A 309 ASP cc_start: 0.8067 (p0) cc_final: 0.7853 (p0) REVERT: E 51 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8391 (tp) outliers start: 22 outliers final: 14 residues processed: 126 average time/residue: 0.5271 time to fit residues: 70.8828 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.0050 chunk 98 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101510 restraints weight = 10994.361| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.30 r_work: 0.3193 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8719 Z= 0.099 Angle : 0.498 6.608 11848 Z= 0.261 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.148 43.107 1214 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.03 % Allowed : 16.89 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.82 (0.26), residues: 1105 helix: 2.72 (0.27), residues: 369 sheet: -0.01 (0.30), residues: 302 loop : -0.98 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8716) covalent geometry : angle 0.49793 / 0.26 (11842) SS BOND : bond 0.00408 / 0.20 ( 3) SS BOND : angle 0.52832 / 0.30 ( 6) hydrogen bonds : bond 0.03639 / 2.38 ( 398) hydrogen bonds : angle 3.85682 / 2.70 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.324 Fit side-chains REVERT: A 33 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: E 51 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8311 (tp) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 0.5315 time to fit residues: 72.4212 Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098600 restraints weight = 10604.435| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.25 r_work: 0.3156 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8719 Z= 0.095 Angle : 0.493 6.713 11848 Z= 0.258 Chirality : 0.040 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.051 41.225 1214 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 16.89 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1105 helix: 2.81 (0.27), residues: 369 sheet: 0.04 (0.30), residues: 303 loop : -0.89 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8716) covalent geometry : angle 0.49338 / 0.26 (11842) SS BOND : bond 0.00430 / 0.21 ( 3) SS BOND : angle 0.58566 / 0.33 ( 6) hydrogen bonds : bond 0.03577 / 2.34 ( 398) hydrogen bonds : angle 3.81330 / 2.67 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.334 Fit side-chains REVERT: B 247 ASP cc_start: 0.7815 (t0) cc_final: 0.7544 (t0) REVERT: A 33 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: A 182 THR cc_start: 0.7234 (p) cc_final: 0.6952 (t) REVERT: A 247 MET cc_start: 0.8414 (mtt) cc_final: 0.8205 (mtm) REVERT: E 51 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8342 (tp) outliers start: 17 outliers final: 11 residues processed: 127 average time/residue: 0.5417 time to fit residues: 73.3989 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 52 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094606 restraints weight = 10697.178| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.29 r_work: 0.3146 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8719 Z= 0.137 Angle : 0.549 7.717 11848 Z= 0.285 Chirality : 0.042 0.152 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.322 41.778 1214 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 17.79 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.91 (0.26), residues: 1105 helix: 2.76 (0.27), residues: 369 sheet: 0.05 (0.30), residues: 302 loop : -0.90 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.013 0.001 TYR E 178 PHE 0.012 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 8716) covalent geometry : angle 0.54930 / 0.28 (11842) SS BOND : bond 0.00519 / 0.25 ( 3) SS BOND : angle 0.75563 / 0.43 ( 6) hydrogen bonds : bond 0.04305 / 2.82 ( 398) hydrogen bonds : angle 3.96288 / 2.78 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.37 seconds wall clock time: 53 minutes 19.59 seconds (3199.59 seconds total)