Starting phenix.real_space_refine on Sat Jun 6 06:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609.map" model { file = "/net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9om7_70609/06_2026/9om7_70609_trim.cif" } resolution = 3.3 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= 0.003 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 18 5.16 5 C 8302 2.51 5 N 2270 2.21 5 O 2528 1.98 5 H 12917 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26047 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4294 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain: "E" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4294 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain: "B" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4294 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain: "D" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4293 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain: "A" Number of atoms: 4294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4294 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain: "C" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4308 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 252} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.19 Number of scatterers: 26047 At special positions: 0 Unit cell: (132.89, 120.28, 69.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 12 15.00 O 2528 8.00 N 2270 7.00 C 8302 6.00 H 12917 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.28 Conformation dependent library (CDL) restraints added in 827.7 milliseconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3014 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 16 sheets defined 35.9% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'F' and resid 124 through 129 removed outlier: 4.387A pdb=" N LEU F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 153 removed outlier: 3.560A pdb=" N LYS F 148 " --> pdb=" O GLN F 144 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 149 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 removed outlier: 3.724A pdb=" N ASP F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'F' and resid 158 through 177 Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 189 through 200 removed outlier: 3.645A pdb=" N LYS F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 243 removed outlier: 3.914A pdb=" N LEU F 240 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 267 removed outlier: 4.526A pdb=" N GLN F 265 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 308 Processing helix chain 'F' and resid 322 through 332 removed outlier: 4.015A pdb=" N ARG F 330 " --> pdb=" O PHE F 326 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 153 removed outlier: 3.554A pdb=" N ASN E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 157 Processing helix chain 'E' and resid 158 through 177 removed outlier: 4.037A pdb=" N VAL E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.529A pdb=" N MET E 243 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 265 removed outlier: 3.571A pdb=" N SER E 264 " --> pdb=" O GLN E 261 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN E 265 " --> pdb=" O ASP E 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 265' Processing helix chain 'E' and resid 286 through 308 removed outlier: 3.816A pdb=" N LYS E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.832A pdb=" N PHE E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 327 " --> pdb=" O CYS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'B' and resid 142 through 153 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 158 through 177 removed outlier: 3.973A pdb=" N VAL B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.933A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 261 through 266 removed outlier: 4.279A pdb=" N GLN B 265 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 308 removed outlier: 3.591A pdb=" N ASN B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.878A pdb=" N PHE B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 327 " --> pdb=" O CYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.678A pdb=" N LYS D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 Processing helix chain 'D' and resid 158 through 177 removed outlier: 3.900A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 261 through 265 removed outlier: 4.243A pdb=" N GLN D 265 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 308 removed outlier: 3.616A pdb=" N LYS D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 331 removed outlier: 4.245A pdb=" N ARG D 330 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 158 through 177 removed outlier: 3.699A pdb=" N VAL A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.563A pdb=" N ALA A 239 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 4.512A pdb=" N GLN A 265 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 removed outlier: 3.543A pdb=" N ASN A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.789A pdb=" N PHE A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 327 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.807A pdb=" N ASN A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 361 " --> pdb=" O LYS A 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 361' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 142 through 153 removed outlier: 3.708A pdb=" N LYS C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 removed outlier: 3.855A pdb=" N ASP C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 157' Processing helix chain 'C' and resid 158 through 177 removed outlier: 3.960A pdb=" N VAL C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 237 through 243 removed outlier: 4.017A pdb=" N ALA C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 243' Processing helix chain 'C' and resid 286 through 308 removed outlier: 3.531A pdb=" N ILE C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing sheet with id=AA1, first strand: chain 'F' and resid 136 through 141 removed outlier: 6.020A pdb=" N ILE F 108 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG F 138 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE F 110 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE F 140 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN F 112 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR F 109 " --> pdb=" O GLY F 183 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR F 185 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU F 111 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE F 187 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE F 113 " --> pdb=" O ILE F 187 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG F 182 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR F 209 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR F 184 " --> pdb=" O TYR F 209 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG F 211 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N GLY F 186 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 232 through 233 removed outlier: 3.648A pdb=" N ASN F 232 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS F 251 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA F 248 " --> pdb=" O HIS F 315 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU F 317 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 232 through 233 removed outlier: 3.648A pdb=" N ASN F 232 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS F 251 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR F 343 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE F 318 " --> pdb=" O TYR F 343 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR F 345 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER F 342 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TRP F 352 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU F 346 " --> pdb=" O TYR F 350 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR F 350 " --> pdb=" O GLU F 346 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE F 365 " --> pdb=" O GLY F 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 136 through 141 removed outlier: 6.334A pdb=" N TYR E 109 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N THR E 185 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU E 111 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE E 187 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 113 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG E 182 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N TYR E 209 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR E 184 " --> pdb=" O TYR E 209 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG E 211 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N GLY E 186 " --> pdb=" O ARG E 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 232 through 233 removed outlier: 8.509A pdb=" N VAL E 272 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 249 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU E 274 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS E 251 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 343 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE E 318 " --> pdb=" O TYR E 343 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR E 345 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE E 340 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE E 355 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER E 342 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY E 353 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN E 344 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 365 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 141 removed outlier: 6.567A pdb=" N ILE B 110 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE B 140 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B 112 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 111 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE B 187 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 113 " --> pdb=" O ILE B 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.539A pdb=" N ASN B 232 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 275 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL B 272 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 249 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU B 274 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS B 251 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 343 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP B 352 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 346 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 136 through 141 removed outlier: 6.159A pdb=" N ILE D 108 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG D 138 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE D 110 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE D 140 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN D 112 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR D 109 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR D 185 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 111 " --> pdb=" O THR D 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 209 through 211 Processing sheet with id=AB2, first strand: chain 'D' and resid 232 through 233 removed outlier: 8.372A pdb=" N VAL D 272 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 249 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU D 274 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS D 251 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 343 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE D 318 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR D 345 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE D 340 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE D 355 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 342 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D 353 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN D 344 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 365 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.814A pdb=" N ILE A 108 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 138 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 110 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 140 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN A 112 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR A 109 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR A 185 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU A 111 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 187 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 113 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR A 209 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 184 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ARG A 211 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N GLY A 186 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 231 through 233 removed outlier: 8.357A pdb=" N VAL A 272 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 249 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 274 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS A 251 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 276 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER A 253 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 343 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE A 318 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR A 345 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 340 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE A 355 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 342 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 353 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLN A 344 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A 351 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 135 through 141 removed outlier: 6.472A pdb=" N ILE C 108 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG C 138 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 110 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 140 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 112 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 187 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 113 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 135 through 141 removed outlier: 6.472A pdb=" N ILE C 108 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG C 138 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 110 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 140 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 112 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG C 182 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR C 209 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR C 184 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ARG C 211 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 217 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 233 removed outlier: 3.807A pdb=" N ASN C 232 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 275 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL C 272 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 249 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU C 274 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS C 251 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA C 248 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU C 317 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 250 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER C 319 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 252 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 343 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C 318 " --> pdb=" O TYR C 343 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR C 345 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE C 340 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 355 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER C 342 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 353 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN C 344 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 365 " --> pdb=" O GLY C 353 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1125 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: 5.76 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12911 1.03 - 1.23: 13 1.23 - 1.42: 5545 1.42 - 1.61: 7800 1.61 - 1.81: 54 Bond restraints: 26323 Sorted by residual: bond pdb=" C36 1SY B 401 " pdb=" N42 1SY B 401 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C36 1SY E 401 " pdb=" N42 1SY E 401 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C36 1SY A 401 " pdb=" N42 1SY A 401 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C36 1SY F 401 " pdb=" N42 1SY F 401 " ideal model delta sigma weight residual 1.357 1.496 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C36 1SY C 401 " pdb=" N42 1SY C 401 " ideal model delta sigma weight residual 1.357 1.495 -0.138 2.00e-02 2.50e+03 4.79e+01 ... (remaining 26318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 47400 4.05 - 8.09: 109 8.09 - 12.14: 48 12.14 - 16.18: 21 16.18 - 20.23: 12 Bond angle restraints: 47590 Sorted by residual: angle pdb=" O19 1SY C 401 " pdb=" P18 1SY C 401 " pdb=" O44 1SY C 401 " ideal model delta sigma weight residual 123.21 102.98 20.23 3.00e+00 1.11e-01 4.55e+01 angle pdb=" O19 1SY F 401 " pdb=" P18 1SY F 401 " pdb=" O44 1SY F 401 " ideal model delta sigma weight residual 123.21 103.01 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O19 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O44 1SY A 401 " ideal model delta sigma weight residual 123.21 103.13 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" O19 1SY D 401 " pdb=" P18 1SY D 401 " pdb=" O44 1SY D 401 " ideal model delta sigma weight residual 123.21 103.16 20.05 3.00e+00 1.11e-01 4.47e+01 angle pdb=" O19 1SY E 401 " pdb=" P18 1SY E 401 " pdb=" O44 1SY E 401 " ideal model delta sigma weight residual 123.21 103.55 19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 47585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11902 35.30 - 70.60: 540 70.60 - 105.91: 68 105.91 - 141.21: 29 141.21 - 176.51: 18 Dihedral angle restraints: 12557 sinusoidal: 7130 harmonic: 5427 Sorted by residual: dihedral pdb=" C3' 1SY E 401 " pdb=" C16 1SY E 401 " pdb=" C4' 1SY E 401 " pdb=" O17 1SY E 401 " ideal model delta sinusoidal sigma weight residual 310.32 133.81 176.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O17 1SY E 401 " pdb=" C16 1SY E 401 " pdb=" C4' 1SY E 401 " pdb=" O4' 1SY E 401 " ideal model delta sinusoidal sigma weight residual -68.57 105.02 -173.59 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3' 1SY B 401 " pdb=" C16 1SY B 401 " pdb=" C4' 1SY B 401 " pdb=" O17 1SY B 401 " ideal model delta sinusoidal sigma weight residual 310.32 137.59 172.73 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1570 0.041 - 0.082: 272 0.082 - 0.124: 141 0.124 - 0.165: 21 0.165 - 0.206: 13 Chirality restraints: 2017 Sorted by residual: chirality pdb=" C2' 1SY C 401 " pdb=" C1' 1SY C 401 " pdb=" C3' 1SY C 401 " pdb=" O2' 1SY C 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C2' 1SY F 401 " pdb=" C1' 1SY F 401 " pdb=" C3' 1SY F 401 " pdb=" O2' 1SY F 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2' 1SY B 401 " pdb=" C1' 1SY B 401 " pdb=" C3' 1SY B 401 " pdb=" O2' 1SY B 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2014 not shown) Planarity restraints: 3824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 313 " 0.165 9.50e-02 1.11e+02 5.54e-02 3.97e+00 pdb=" NE ARG A 313 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 313 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 313 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 313 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 313 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 313 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 313 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO F 168 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" N LYS F 169 " -0.029 2.00e-02 2.50e+03 pdb=" CA LYS F 169 " 0.007 2.00e-02 2.50e+03 pdb=" H LYS F 169 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 159 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 160 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.023 5.00e-02 4.00e+02 ... (remaining 3821 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1221 2.19 - 2.79: 51383 2.79 - 3.39: 66714 3.39 - 4.00: 91284 4.00 - 4.60: 142085 Nonbonded interactions: 352687 Sorted by model distance: nonbonded pdb=" O ASN B 152 " pdb="HD21 ASN B 152 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLN B 244 " pdb=" H GLN B 244 " model vdw 1.599 2.450 nonbonded pdb=" O PHE B 173 " pdb=" HG SER B 177 " model vdw 1.608 2.450 nonbonded pdb=" HG1 THR B 255 " pdb=" O SER B 319 " model vdw 1.613 2.450 nonbonded pdb=" H ASN F 347 " pdb=" O THR E 335 " model vdw 1.636 2.450 ... (remaining 352682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 107 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 202 through 401)) selection = (chain 'B' and (resid 107 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 202 through 401)) selection = (chain 'C' and ((resid 107 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12 or name HH21 or name HH22)) or resid 108 through 20 \ 0 or (resid 201 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 202 throu \ gh 401)) selection = chain 'D' selection = (chain 'E' and (resid 107 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 202 through 401)) selection = (chain 'F' and (resid 107 through 200 or (resid 201 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 202 through 401)) } 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: 1.290 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: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.650 Find NCS groups from input model: 0.470 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.008 0.139 13406 Z= 0.410 Angle : 1.068 20.229 18179 Z= 0.403 Chirality : 0.044 0.206 2017 Planarity : 0.003 0.073 2318 Dihedral : 23.838 176.512 5415 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.14 % Allowed : 25.37 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1561 helix: 3.08 (0.26), residues: 430 sheet: -0.83 (0.27), residues: 434 loop : -1.13 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 313 TYR 0.009 0.001 TYR F 228 PHE 0.009 0.001 PHE A 146 TRP 0.013 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.41 (13406) covalent geometry : angle 1.06780 / 0.40 (18179) hydrogen bonds : bond 0.22155 / 15.06 ( 394) hydrogen bonds : angle 6.71246 / 4.92 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASP cc_start: 0.7831 (m-30) cc_final: 0.7570 (m-30) REVERT: D 360 ASN cc_start: 0.8015 (m-40) cc_final: 0.7714 (m-40) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.3878 time to fit residues: 59.2658 Evaluate side-chains 110 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 162 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104145 restraints weight = 52140.970| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.64 r_work: 0.2912 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13406 Z= 0.115 Angle : 0.519 5.368 18179 Z= 0.271 Chirality : 0.043 0.150 2017 Planarity : 0.004 0.045 2318 Dihedral : 26.234 179.742 2109 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.11 % Allowed : 23.90 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.23), residues: 1561 helix: 2.79 (0.25), residues: 447 sheet: -0.89 (0.27), residues: 434 loop : -1.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.010 0.001 TYR E 298 PHE 0.014 0.001 PHE E 146 TRP 0.011 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13406) covalent geometry : angle 0.51943 / 0.27 (18179) hydrogen bonds : bond 0.05572 / 3.79 ( 394) hydrogen bonds : angle 5.00031 / 3.68 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 134 ASP cc_start: 0.7839 (m-30) cc_final: 0.7455 (m-30) REVERT: D 360 ASN cc_start: 0.8049 (m-40) cc_final: 0.7730 (m-40) REVERT: C 126 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7403 (tptm) outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 0.3731 time to fit residues: 64.5527 Evaluate side-chains 115 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.087451 restraints weight = 56729.513| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.58 r_work: 0.2981 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13406 Z= 0.155 Angle : 0.536 5.791 18179 Z= 0.275 Chirality : 0.043 0.150 2017 Planarity : 0.004 0.048 2318 Dihedral : 25.879 179.789 2109 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.74 % Allowed : 23.48 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1561 helix: 2.58 (0.25), residues: 452 sheet: -0.98 (0.26), residues: 432 loop : -1.26 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.010 0.001 TYR A 298 PHE 0.014 0.001 PHE A 146 TRP 0.012 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13406) covalent geometry : angle 0.53597 / 0.27 (18179) hydrogen bonds : bond 0.05450 / 3.69 ( 394) hydrogen bonds : angle 4.73405 / 3.47 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8144 (m-40) cc_final: 0.7833 (m-40) REVERT: A 152 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.8032 (t0) REVERT: C 126 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7494 (tptm) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.3644 time to fit residues: 65.1867 Evaluate side-chains 124 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 185 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.086571 restraints weight = 56810.965| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.58 r_work: 0.2841 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13406 Z= 0.157 Angle : 0.540 6.184 18179 Z= 0.277 Chirality : 0.043 0.151 2017 Planarity : 0.004 0.049 2318 Dihedral : 25.736 179.699 2107 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 24.11 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1561 helix: 2.51 (0.25), residues: 452 sheet: -1.05 (0.26), residues: 432 loop : -1.30 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.010 0.001 TYR A 298 PHE 0.015 0.001 PHE A 146 TRP 0.013 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13406) covalent geometry : angle 0.53962 / 0.28 (18179) hydrogen bonds : bond 0.05167 / 3.50 ( 394) hydrogen bonds : angle 4.62855 / 3.40 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8192 (m-40) cc_final: 0.7859 (m-40) REVERT: A 152 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8045 (t0) REVERT: C 126 LYS cc_start: 0.7724 (tppt) cc_final: 0.7453 (tptm) REVERT: C 238 GLN cc_start: 0.8268 (tp40) cc_final: 0.7730 (tm-30) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 0.3738 time to fit residues: 64.9433 Evaluate side-chains 129 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 268 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 0.0370 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.086508 restraints weight = 56988.076| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.58 r_work: 0.2973 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13406 Z= 0.170 Angle : 0.552 6.459 18179 Z= 0.282 Chirality : 0.043 0.160 2017 Planarity : 0.004 0.054 2318 Dihedral : 25.660 179.510 2107 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.53 % Allowed : 23.97 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1561 helix: 2.46 (0.25), residues: 452 sheet: -1.09 (0.26), residues: 432 loop : -1.33 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.010 0.001 TYR A 298 PHE 0.015 0.001 PHE A 146 TRP 0.014 0.002 TRP A 352 HIS 0.003 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (13406) covalent geometry : angle 0.55234 / 0.28 (18179) hydrogen bonds : bond 0.05194 / 3.51 ( 394) hydrogen bonds : angle 4.58947 / 3.36 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8185 (m-40) cc_final: 0.7866 (m-40) REVERT: A 152 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8142 (t0) REVERT: C 126 LYS cc_start: 0.7781 (tppt) cc_final: 0.7543 (tptm) REVERT: C 238 GLN cc_start: 0.8275 (tp40) cc_final: 0.7742 (tm-30) outliers start: 22 outliers final: 17 residues processed: 129 average time/residue: 0.3704 time to fit residues: 63.5643 Evaluate side-chains 126 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 268 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.088754 restraints weight = 56488.063| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.58 r_work: 0.2860 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13406 Z= 0.095 Angle : 0.495 5.601 18179 Z= 0.254 Chirality : 0.042 0.148 2017 Planarity : 0.004 0.058 2318 Dihedral : 25.180 178.356 2107 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.60 % Allowed : 23.76 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1561 helix: 2.73 (0.25), residues: 452 sheet: -1.00 (0.26), residues: 432 loop : -1.24 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.009 0.001 TYR A 298 PHE 0.015 0.001 PHE E 133 TRP 0.014 0.001 TRP A 352 HIS 0.003 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.09 (13406) covalent geometry : angle 0.49503 / 0.25 (18179) hydrogen bonds : bond 0.04172 / 2.83 ( 394) hydrogen bonds : angle 4.40336 / 3.23 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8109 (m-40) cc_final: 0.7789 (m-40) REVERT: A 152 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (t0) REVERT: C 126 LYS cc_start: 0.7673 (tppt) cc_final: 0.7446 (tptm) REVERT: C 238 GLN cc_start: 0.8286 (tp40) cc_final: 0.7738 (tm-30) outliers start: 23 outliers final: 18 residues processed: 134 average time/residue: 0.3529 time to fit residues: 63.8863 Evaluate side-chains 128 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 268 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.088468 restraints weight = 56420.988| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.57 r_work: 0.2861 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13406 Z= 0.113 Angle : 0.507 5.886 18179 Z= 0.258 Chirality : 0.042 0.155 2017 Planarity : 0.004 0.064 2318 Dihedral : 24.929 179.290 2107 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.67 % Allowed : 23.83 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1561 helix: 2.70 (0.25), residues: 452 sheet: -0.99 (0.26), residues: 432 loop : -1.24 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.009 0.001 TYR A 298 PHE 0.013 0.001 PHE A 146 TRP 0.012 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (13406) covalent geometry : angle 0.50662 / 0.26 (18179) hydrogen bonds : bond 0.04280 / 2.90 ( 394) hydrogen bonds : angle 4.37098 / 3.20 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8129 (m-40) cc_final: 0.7822 (m-40) REVERT: A 152 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8015 (t0) REVERT: C 126 LYS cc_start: 0.7655 (tppt) cc_final: 0.7449 (tptm) REVERT: C 238 GLN cc_start: 0.8266 (tp40) cc_final: 0.7719 (tm-30) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.3559 time to fit residues: 63.2092 Evaluate side-chains 130 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 268 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.093949 restraints weight = 54680.783| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.66 r_work: 0.2871 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13406 Z= 0.178 Angle : 0.564 8.071 18179 Z= 0.286 Chirality : 0.044 0.200 2017 Planarity : 0.004 0.069 2318 Dihedral : 25.230 178.766 2107 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.74 % Allowed : 23.76 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1561 helix: 2.46 (0.25), residues: 452 sheet: -1.05 (0.26), residues: 432 loop : -1.34 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.012 0.001 TYR F 228 PHE 0.015 0.001 PHE A 146 TRP 0.012 0.002 TRP A 352 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (13406) covalent geometry : angle 0.56371 / 0.29 (18179) hydrogen bonds : bond 0.05070 / 3.42 ( 394) hydrogen bonds : angle 4.44749 / 3.25 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8203 (m-40) cc_final: 0.7914 (m-40) REVERT: A 152 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8140 (t0) REVERT: C 126 LYS cc_start: 0.7720 (tppt) cc_final: 0.7509 (tptm) REVERT: C 238 GLN cc_start: 0.8321 (tp40) cc_final: 0.7781 (tm-30) outliers start: 25 outliers final: 18 residues processed: 129 average time/residue: 0.3735 time to fit residues: 64.4575 Evaluate side-chains 127 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.086790 restraints weight = 56646.526| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.57 r_work: 0.2837 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13406 Z= 0.147 Angle : 0.542 6.653 18179 Z= 0.277 Chirality : 0.043 0.185 2017 Planarity : 0.004 0.074 2318 Dihedral : 25.221 179.409 2107 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.74 % Allowed : 23.83 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1561 helix: 2.50 (0.25), residues: 452 sheet: -1.06 (0.26), residues: 432 loop : -1.34 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 313 TYR 0.010 0.001 TYR F 228 PHE 0.015 0.001 PHE A 146 TRP 0.014 0.001 TRP A 352 HIS 0.003 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13406) covalent geometry : angle 0.54154 / 0.28 (18179) hydrogen bonds : bond 0.04806 / 3.26 ( 394) hydrogen bonds : angle 4.41235 / 3.24 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 360 ASN cc_start: 0.8179 (m-40) cc_final: 0.7855 (m-40) REVERT: A 152 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8042 (t0) REVERT: C 126 LYS cc_start: 0.7651 (tppt) cc_final: 0.7451 (tptm) REVERT: C 238 GLN cc_start: 0.8314 (tp40) cc_final: 0.7768 (tm-30) outliers start: 25 outliers final: 24 residues processed: 128 average time/residue: 0.3646 time to fit residues: 62.5164 Evaluate side-chains 130 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.089596 restraints weight = 55924.820| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.57 r_work: 0.2873 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 13406 Z= 0.092 Angle : 0.488 5.644 18179 Z= 0.251 Chirality : 0.042 0.150 2017 Planarity : 0.004 0.070 2318 Dihedral : 24.653 179.401 2107 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.39 % Allowed : 24.11 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1561 helix: 2.82 (0.25), residues: 452 sheet: -0.96 (0.26), residues: 432 loop : -1.23 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 313 TYR 0.009 0.001 TYR F 228 PHE 0.012 0.001 PHE A 146 TRP 0.016 0.001 TRP A 352 HIS 0.003 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.09 (13406) covalent geometry : angle 0.48830 / 0.25 (18179) hydrogen bonds : bond 0.03811 / 2.60 ( 394) hydrogen bonds : angle 4.23385 / 3.12 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 134 ASP cc_start: 0.7856 (m-30) cc_final: 0.7495 (m-30) REVERT: D 360 ASN cc_start: 0.8039 (m-40) cc_final: 0.7715 (m-40) REVERT: A 152 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8050 (t0) REVERT: C 238 GLN cc_start: 0.8292 (tp40) cc_final: 0.7747 (tm-30) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.3636 time to fit residues: 65.5021 Evaluate side-chains 129 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 203 HIS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108454 restraints weight = 51972.456| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.63 r_work: 0.2926 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 13406 Z= 0.092 Angle : 0.488 5.882 18179 Z= 0.250 Chirality : 0.042 0.164 2017 Planarity : 0.004 0.075 2318 Dihedral : 24.404 179.389 2107 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.46 % Allowed : 24.04 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1561 helix: 2.84 (0.25), residues: 452 sheet: -0.91 (0.26), residues: 432 loop : -1.20 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 313 TYR 0.009 0.001 TYR F 228 PHE 0.011 0.001 PHE A 146 TRP 0.012 0.001 TRP A 352 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.09 (13406) covalent geometry : angle 0.48787 / 0.25 (18179) hydrogen bonds : bond 0.03780 / 2.58 ( 394) hydrogen bonds : angle 4.18662 / 3.09 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.42 seconds wall clock time: 93 minutes 31.72 seconds (5611.72 seconds total)