Starting phenix.real_space_refine on Mon Sep 14 18:34:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pp8_20422/09_2026/6pp8_20422.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10120 2.51 5 N 2720 2.21 5 O 3209 1.98 5 H 16234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32335 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5273 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 2 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5409 Classifications: {'peptide': 351} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain breaks: 1 Chain: "C" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5396 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "D" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5377 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5395 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 2 Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5244 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 59 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.18 Number of scatterers: 32335 At special positions: 0 Unit cell: (146.16, 140.36, 102.08, 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 35 16.00 P 17 15.00 O 3209 8.00 N 2720 7.00 C 10120 6.00 H 16234 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 951.9 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 53.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.706A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.790A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 158 through 170 removed outlier: 4.101A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.540A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.642A pdb=" N GLN A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.583A pdb=" N GLY A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 4.066A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.891A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 299' Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.514A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.679A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.547A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.815A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.580A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.915A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.791A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.565A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.692A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.506A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.577A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.597A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 195 " --> pdb=" O LYS B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.926A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.707A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.737A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.598A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.570A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.838A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.735A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.779A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.726A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.809A pdb=" N LYS C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.542A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 4.161A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.508A pdb=" N LYS C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.904A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.829A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.868A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.673A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 307 removed outlier: 3.770A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.648A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.717A pdb=" N LEU C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.006A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.638A pdb=" N ALA C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.844A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.706A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.906A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.618A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.543A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.877A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.927A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.716A pdb=" N ALA D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.605A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.753A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.691A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 3.675A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.529A pdb=" N LEU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.742A pdb=" N ALA D 379 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.661A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.674A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.524A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.553A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.553A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.652A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.554A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.783A pdb=" N ILE E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 343 removed outlier: 3.685A pdb=" N LEU E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 removed outlier: 4.085A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 371 Processing helix chain 'E' and resid 372 through 380 removed outlier: 3.601A pdb=" N VAL E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.867A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.577A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 102 removed outlier: 3.578A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.640A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 4.126A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 204 through 217 removed outlier: 4.199A pdb=" N GLN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.607A pdb=" N GLY F 227 " --> pdb=" O PRO F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 removed outlier: 4.072A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.989A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.635A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.761A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'F' and resid 332 through 345 removed outlier: 4.031A pdb=" N LEU F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.588A pdb=" N LEU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.547A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.831A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 182 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 115 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.917A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.630A pdb=" N ASP B 184 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.864A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 222 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.760A pdb=" N ILE B 398 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 3.672A pdb=" N THR C 141 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 182 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 349 through 350 removed outlier: 4.019A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 143 through 144 removed outlier: 3.714A pdb=" N ASP D 184 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.062A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144 removed outlier: 3.633A pdb=" N ALA E 143 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP E 184 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.943A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 347 through 348 removed outlier: 6.872A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.745A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.859A pdb=" N ALA F 220 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 238 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.513A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1671 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: 6.67 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 16228 1.05 - 1.27: 2877 1.27 - 1.50: 6185 1.50 - 1.72: 7192 1.72 - 1.95: 59 Bond restraints: 32541 Sorted by residual: bond pdb=" N SER B 62 " pdb=" H1 SER B 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" O3B AGS D 600 " pdb=" PB AGS D 600 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" O3B AGS E 600 " pdb=" PB AGS E 600 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O3B AGS A 600 " pdb=" PB AGS A 600 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS B 600 " pdb=" PB AGS B 600 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 32536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 58200 2.06 - 4.12: 821 4.12 - 6.18: 111 6.18 - 8.25: 23 8.25 - 10.31: 19 Bond angle restraints: 59174 Sorted by residual: angle pdb=" N ALA F 151 " pdb=" CA ALA F 151 " pdb=" C ALA F 151 " ideal model delta sigma weight residual 111.24 119.64 -8.40 1.38e+00 5.25e-01 3.71e+01 angle pdb=" N SER E 266 " pdb=" CA SER E 266 " pdb=" C SER E 266 " ideal model delta sigma weight residual 109.72 115.67 -5.95 1.60e+00 3.91e-01 1.38e+01 angle pdb=" N GLY F 265 " pdb=" CA GLY F 265 " pdb=" C GLY F 265 " ideal model delta sigma weight residual 113.18 104.69 8.49 2.37e+00 1.78e-01 1.28e+01 angle pdb=" PB AGS D 600 " pdb=" O3B AGS D 600 " pdb=" PG AGS D 600 " ideal model delta sigma weight residual 129.21 118.90 10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CA GLN D 233 " pdb=" C GLN D 233 " pdb=" O GLN D 233 " ideal model delta sigma weight residual 121.84 117.87 3.97 1.16e+00 7.43e-01 1.17e+01 ... (remaining 59169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 14625 30.26 - 60.52: 512 60.52 - 90.78: 21 90.78 - 121.03: 2 121.03 - 151.29: 8 Dihedral angle restraints: 15168 sinusoidal: 8664 harmonic: 6504 Sorted by residual: dihedral pdb=" O1A AGS A 600 " pdb=" O3A AGS A 600 " pdb=" PA AGS A 600 " pdb=" PB AGS A 600 " ideal model delta sinusoidal sigma weight residual 82.37 -68.92 151.29 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A AGS C 600 " pdb=" O3A AGS C 600 " pdb=" PA AGS C 600 " pdb=" PB AGS C 600 " ideal model delta sinusoidal sigma weight residual 82.37 -56.56 138.93 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" O1A AGS D 600 " pdb=" O3A AGS D 600 " pdb=" PA AGS D 600 " pdb=" PB AGS D 600 " ideal model delta sinusoidal sigma weight residual 82.37 -54.30 136.67 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2071 0.051 - 0.102: 402 0.102 - 0.152: 116 0.152 - 0.203: 5 0.203 - 0.254: 5 Chirality restraints: 2599 Sorted by residual: chirality pdb=" C3' AGS E 600 " pdb=" C2' AGS E 600 " pdb=" C4' AGS E 600 " pdb=" O3' AGS E 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' AGS C 600 " pdb=" C2' AGS C 600 " pdb=" C4' AGS C 600 " pdb=" O3' AGS C 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' AGS B 600 " pdb=" C2' AGS B 600 " pdb=" C4' AGS B 600 " pdb=" O3' AGS B 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2596 not shown) Planarity restraints: 4828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 307 " 0.600 9.50e-02 1.11e+02 2.00e-01 4.23e+01 pdb=" NE ARG D 307 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 307 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 307 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 307 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG D 307 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG D 307 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG D 307 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG D 307 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 123 " -0.029 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C SER E 123 " 0.101 2.00e-02 2.50e+03 pdb=" O SER E 123 " -0.038 2.00e-02 2.50e+03 pdb=" N GLY E 124 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.325 9.50e-02 1.11e+02 1.08e-01 1.24e+01 pdb=" NE ARG A 98 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.007 2.00e-02 2.50e+03 ... (remaining 4825 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 151 2.02 - 2.67: 47795 2.67 - 3.31: 90896 3.31 - 3.96: 111576 3.96 - 4.60: 177381 Nonbonded interactions: 427799 Sorted by model distance: nonbonded pdb=" HH TYR F 96 " pdb=" O ARG F 178 " model vdw 1.379 2.450 nonbonded pdb=" O GLU B 263 " pdb=" HG1 THR B 264 " model vdw 1.450 2.450 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.463 2.450 nonbonded pdb=" HZ3 LYS F 125 " pdb=" O1B ADP F 600 " model vdw 1.493 2.450 nonbonded pdb=" O LEU B 326 " pdb=" HG1 THR B 334 " model vdw 1.540 2.450 ... (remaining 427794 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 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'B' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'C' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'D' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'E' and (resid 65 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 192 or resid 201 through 227 or resid 233 through 413)) selection = (chain 'F' and (resid 65 through 192 or resid 201 through 227 or resid 233 throu \ gh 259 or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 261 through 41 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.230 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.230 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 16308 Z= 0.226 Angle : 0.822 10.307 22075 Z= 0.421 Chirality : 0.045 0.254 2599 Planarity : 0.007 0.258 2840 Dihedral : 13.647 151.293 6284 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.36 (0.16), residues: 2047 helix: -1.87 (0.15), residues: 728 sheet: -1.64 (0.27), residues: 272 loop : -1.20 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.017 0.001 TYR F 96 PHE 0.008 0.001 PHE A 140 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (16307) covalent geometry : angle 0.82204 / 0.42 (22075) hydrogen bonds : bond 0.31071 / 21.21 ( 594) hydrogen bonds : angle 8.24533 / 5.78 ( 1671) Misc. bond : bond 0.02214 / 1.48 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7941 (t80) cc_final: 0.7626 (t80) REVERT: A 245 PHE cc_start: 0.5181 (m-80) cc_final: 0.4942 (m-80) REVERT: A 287 LEU cc_start: 0.8856 (mt) cc_final: 0.8632 (mp) REVERT: A 317 LEU cc_start: 0.7186 (mt) cc_final: 0.6917 (mt) REVERT: B 140 PHE cc_start: 0.7262 (t80) cc_final: 0.5583 (t80) REVERT: B 141 THR cc_start: 0.9447 (t) cc_final: 0.8968 (p) REVERT: B 279 ASP cc_start: 0.8742 (m-30) cc_final: 0.8401 (t0) REVERT: B 293 GLU cc_start: 0.9011 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 393 VAL cc_start: 0.8875 (t) cc_final: 0.8625 (t) REVERT: C 136 LEU cc_start: 0.8758 (tp) cc_final: 0.8483 (tp) REVERT: C 294 ASP cc_start: 0.8891 (m-30) cc_final: 0.8658 (m-30) REVERT: C 319 GLU cc_start: 0.8956 (pt0) cc_final: 0.8724 (pm20) REVERT: C 352 ASP cc_start: 0.8824 (p0) cc_final: 0.8321 (t0) REVERT: C 366 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9237 (mmmt) REVERT: D 130 GLU cc_start: 0.9107 (tt0) cc_final: 0.8331 (tm-30) REVERT: D 182 TYR cc_start: 0.8926 (t80) cc_final: 0.8327 (t80) REVERT: D 201 ASP cc_start: 0.8918 (m-30) cc_final: 0.8409 (p0) REVERT: D 256 LYS cc_start: 0.8699 (mttt) cc_final: 0.8424 (mmmt) REVERT: D 285 GLU cc_start: 0.8643 (tp30) cc_final: 0.8401 (tp30) REVERT: E 69 GLU cc_start: 0.9252 (tt0) cc_final: 0.8996 (mt-10) REVERT: E 144 ASP cc_start: 0.7931 (t0) cc_final: 0.6479 (t0) REVERT: E 170 ASP cc_start: 0.8494 (m-30) cc_final: 0.8261 (t70) REVERT: E 184 ASP cc_start: 0.8268 (p0) cc_final: 0.8018 (p0) REVERT: E 205 GLU cc_start: 0.8384 (tt0) cc_final: 0.7758 (tm-30) REVERT: E 208 GLN cc_start: 0.8530 (mt0) cc_final: 0.8305 (mt0) REVERT: E 213 LYS cc_start: 0.8034 (tptp) cc_final: 0.7815 (tptp) REVERT: E 216 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 239 ASP cc_start: 0.8766 (m-30) cc_final: 0.8389 (t0) REVERT: E 245 PHE cc_start: 0.8622 (m-80) cc_final: 0.8372 (m-10) REVERT: E 289 GLN cc_start: 0.8911 (mt0) cc_final: 0.7671 (mt0) REVERT: E 413 TYR cc_start: 0.8572 (m-80) cc_final: 0.7602 (m-80) REVERT: F 130 GLU cc_start: 0.9236 (mt-10) cc_final: 0.9024 (mt-10) REVERT: F 261 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8184 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2838 time to fit residues: 182.1142 Evaluate side-chains 262 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN F 208 GLN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.103047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079447 restraints weight = 153737.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083352 restraints weight = 68005.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085913 restraints weight = 40026.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.087575 restraints weight = 28241.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.088633 restraints weight = 22417.600| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16308 Z= 0.175 Angle : 0.587 5.863 22075 Z= 0.306 Chirality : 0.041 0.164 2599 Planarity : 0.004 0.037 2840 Dihedral : 11.267 179.237 2405 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.18), residues: 2047 helix: -0.49 (0.16), residues: 905 sheet: -1.24 (0.29), residues: 273 loop : -1.15 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 261 TYR 0.020 0.002 TYR F 96 PHE 0.015 0.001 PHE A 341 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16307) covalent geometry : angle 0.58668 / 0.31 (22075) hydrogen bonds : bond 0.05239 / 3.56 ( 594) hydrogen bonds : angle 5.81902 / 4.05 ( 1671) Misc. bond : bond 0.00791 / 0.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8096 (t80) cc_final: 0.7779 (t80) REVERT: A 170 ASP cc_start: 0.9281 (m-30) cc_final: 0.9003 (m-30) REVERT: A 317 LEU cc_start: 0.7173 (mt) cc_final: 0.6807 (mt) REVERT: B 141 THR cc_start: 0.9446 (t) cc_final: 0.9208 (t) REVERT: B 279 ASP cc_start: 0.8683 (m-30) cc_final: 0.8239 (t0) REVERT: B 293 GLU cc_start: 0.8912 (tt0) cc_final: 0.8632 (tm-30) REVERT: B 390 MET cc_start: 0.8454 (tpt) cc_final: 0.8217 (tmm) REVERT: C 136 LEU cc_start: 0.8827 (tp) cc_final: 0.8565 (tp) REVERT: C 243 ILE cc_start: 0.9030 (mt) cc_final: 0.8707 (mm) REVERT: C 352 ASP cc_start: 0.8642 (p0) cc_final: 0.8254 (p0) REVERT: D 130 GLU cc_start: 0.9009 (tt0) cc_final: 0.8366 (tm-30) REVERT: D 190 SER cc_start: 0.8742 (t) cc_final: 0.8392 (p) REVERT: D 256 LYS cc_start: 0.8919 (mttt) cc_final: 0.8698 (mmmt) REVERT: D 356 ASP cc_start: 0.8748 (m-30) cc_final: 0.8455 (m-30) REVERT: E 93 TYR cc_start: 0.8056 (t80) cc_final: 0.7842 (t80) REVERT: E 101 ASN cc_start: 0.8484 (m-40) cc_final: 0.7977 (t0) REVERT: E 170 ASP cc_start: 0.8475 (m-30) cc_final: 0.8060 (t70) REVERT: E 239 ASP cc_start: 0.8895 (m-30) cc_final: 0.8601 (t0) REVERT: E 363 MET cc_start: 0.8798 (mmt) cc_final: 0.8550 (tpp) REVERT: E 387 LEU cc_start: 0.9109 (tp) cc_final: 0.8878 (tt) REVERT: F 182 TYR cc_start: 0.9150 (t80) cc_final: 0.7945 (t80) REVERT: F 184 ASP cc_start: 0.8708 (t70) cc_final: 0.8331 (m-30) REVERT: F 247 CYS cc_start: 0.9131 (m) cc_final: 0.8779 (m) REVERT: F 384 MET cc_start: 0.6646 (mmm) cc_final: 0.6422 (mmm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2571 time to fit residues: 109.6491 Evaluate side-chains 208 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 117 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN C 106 ASN F 232 GLN F 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.103267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079761 restraints weight = 151250.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083623 restraints weight = 67102.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086207 restraints weight = 39550.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.087875 restraints weight = 27762.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.088966 restraints weight = 21949.446| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16308 Z= 0.105 Angle : 0.488 5.893 22075 Z= 0.251 Chirality : 0.039 0.150 2599 Planarity : 0.003 0.027 2840 Dihedral : 10.877 178.542 2405 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.17 % Allowed : 0.70 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.67 (0.18), residues: 2047 helix: 0.21 (0.17), residues: 897 sheet: -0.74 (0.29), residues: 302 loop : -0.92 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 307 TYR 0.014 0.001 TYR A 93 PHE 0.008 0.001 PHE A 341 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (16307) covalent geometry : angle 0.48765 / 0.25 (22075) hydrogen bonds : bond 0.04157 / 2.83 ( 594) hydrogen bonds : angle 5.16317 / 3.60 ( 1671) Misc. bond : bond 0.00610 / 0.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8070 (t80) cc_final: 0.7780 (t80) REVERT: A 317 LEU cc_start: 0.7150 (mt) cc_final: 0.6922 (mt) REVERT: B 188 LYS cc_start: 0.8530 (tttt) cc_final: 0.8094 (ptmt) REVERT: B 279 ASP cc_start: 0.8684 (m-30) cc_final: 0.8205 (t0) REVERT: B 293 GLU cc_start: 0.8907 (tt0) cc_final: 0.8632 (tm-30) REVERT: B 352 ASP cc_start: 0.8261 (p0) cc_final: 0.7998 (p0) REVERT: B 393 VAL cc_start: 0.8728 (t) cc_final: 0.8402 (m) REVERT: C 317 LEU cc_start: 0.8772 (mm) cc_final: 0.8254 (mt) REVERT: C 320 GLU cc_start: 0.8803 (pp20) cc_final: 0.8376 (pp20) REVERT: C 352 ASP cc_start: 0.8560 (p0) cc_final: 0.8184 (p0) REVERT: D 130 GLU cc_start: 0.8999 (tt0) cc_final: 0.8388 (tm-30) REVERT: D 190 SER cc_start: 0.8719 (t) cc_final: 0.8484 (p) REVERT: D 285 GLU cc_start: 0.8506 (tp30) cc_final: 0.8293 (tp30) REVERT: D 356 ASP cc_start: 0.8690 (m-30) cc_final: 0.8378 (m-30) REVERT: E 101 ASN cc_start: 0.8467 (m-40) cc_final: 0.7936 (t0) REVERT: E 170 ASP cc_start: 0.8553 (m-30) cc_final: 0.8067 (t70) REVERT: E 247 CYS cc_start: 0.8411 (m) cc_final: 0.8169 (m) REVERT: E 363 MET cc_start: 0.8680 (mmt) cc_final: 0.8470 (tpp) REVERT: E 387 LEU cc_start: 0.9105 (tp) cc_final: 0.8893 (tt) REVERT: F 182 TYR cc_start: 0.9137 (t80) cc_final: 0.8894 (t80) REVERT: F 247 CYS cc_start: 0.9167 (m) cc_final: 0.8886 (m) outliers start: 3 outliers final: 0 residues processed: 257 average time/residue: 0.2501 time to fit residues: 99.5646 Evaluate side-chains 206 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 182 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.100002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076071 restraints weight = 153818.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079832 restraints weight = 69119.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.082312 restraints weight = 41244.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083915 restraints weight = 29400.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084947 restraints weight = 23609.112| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16308 Z= 0.160 Angle : 0.516 6.085 22075 Z= 0.268 Chirality : 0.040 0.149 2599 Planarity : 0.003 0.029 2840 Dihedral : 10.932 179.014 2405 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.18), residues: 2047 helix: 0.28 (0.17), residues: 905 sheet: -0.52 (0.30), residues: 302 loop : -0.86 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 261 TYR 0.012 0.001 TYR F 96 PHE 0.013 0.001 PHE E 298 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (16307) covalent geometry : angle 0.51610 / 0.27 (22075) hydrogen bonds : bond 0.03471 / 2.36 ( 594) hydrogen bonds : angle 5.16814 / 3.60 ( 1671) Misc. bond : bond 0.00670 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7192 (mt) cc_final: 0.6914 (mt) REVERT: B 140 PHE cc_start: 0.7694 (t80) cc_final: 0.6579 (t80) REVERT: B 141 THR cc_start: 0.9409 (t) cc_final: 0.9121 (t) REVERT: B 142 MET cc_start: 0.8336 (mpp) cc_final: 0.8038 (mpp) REVERT: B 188 LYS cc_start: 0.8523 (tttt) cc_final: 0.8133 (tttp) REVERT: B 279 ASP cc_start: 0.8699 (m-30) cc_final: 0.8176 (t0) REVERT: B 352 ASP cc_start: 0.8324 (p0) cc_final: 0.8041 (p0) REVERT: B 393 VAL cc_start: 0.8803 (t) cc_final: 0.8542 (m) REVERT: C 181 VAL cc_start: 0.9329 (t) cc_final: 0.8843 (m) REVERT: C 352 ASP cc_start: 0.8603 (p0) cc_final: 0.8247 (p0) REVERT: D 130 GLU cc_start: 0.9036 (tt0) cc_final: 0.8407 (tm-30) REVERT: D 142 MET cc_start: 0.8616 (mtt) cc_final: 0.8185 (mmt) REVERT: D 190 SER cc_start: 0.8813 (t) cc_final: 0.8553 (p) REVERT: D 356 ASP cc_start: 0.8775 (m-30) cc_final: 0.8456 (m-30) REVERT: E 101 ASN cc_start: 0.8413 (m-40) cc_final: 0.7917 (t0) REVERT: E 135 LEU cc_start: 0.7812 (tp) cc_final: 0.7471 (tt) REVERT: E 170 ASP cc_start: 0.8624 (m-30) cc_final: 0.8113 (t0) REVERT: E 216 GLU cc_start: 0.8472 (tp30) cc_final: 0.8206 (tm-30) REVERT: E 363 MET cc_start: 0.8667 (mmt) cc_final: 0.8353 (tpp) REVERT: E 377 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8420 (mm-30) REVERT: E 413 TYR cc_start: 0.8240 (m-80) cc_final: 0.7741 (m-80) REVERT: F 216 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7885 (tm-30) REVERT: F 247 CYS cc_start: 0.9204 (m) cc_final: 0.8950 (m) REVERT: F 324 GLN cc_start: 0.9346 (mt0) cc_final: 0.9072 (mm110) REVERT: F 342 ASN cc_start: 0.8034 (m-40) cc_final: 0.7785 (m110) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2499 time to fit residues: 91.6126 Evaluate side-chains 187 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 155 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.101539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077284 restraints weight = 153801.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081089 restraints weight = 68237.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083619 restraints weight = 40501.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.085247 restraints weight = 28751.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.086295 restraints weight = 23030.103| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16308 Z= 0.118 Angle : 0.474 6.079 22075 Z= 0.244 Chirality : 0.039 0.149 2599 Planarity : 0.003 0.031 2840 Dihedral : 10.828 179.645 2405 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 0.58 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.18), residues: 2047 helix: 0.47 (0.17), residues: 914 sheet: -0.31 (0.30), residues: 297 loop : -0.81 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 191 TYR 0.015 0.001 TYR A 337 PHE 0.008 0.001 PHE A 245 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (16307) covalent geometry : angle 0.47423 / 0.24 (22075) hydrogen bonds : bond 0.03165 / 2.15 ( 594) hydrogen bonds : angle 4.96859 / 3.47 ( 1671) Misc. bond : bond 0.00619 / 0.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8198 (t80) cc_final: 0.7980 (t80) REVERT: A 317 LEU cc_start: 0.7106 (mt) cc_final: 0.6883 (mt) REVERT: B 140 PHE cc_start: 0.7669 (t80) cc_final: 0.7417 (t80) REVERT: B 188 LYS cc_start: 0.8535 (tttt) cc_final: 0.8160 (tttp) REVERT: B 352 ASP cc_start: 0.8363 (p0) cc_final: 0.8027 (p0) REVERT: B 390 MET cc_start: 0.8141 (tpt) cc_final: 0.7910 (tpt) REVERT: C 320 GLU cc_start: 0.8771 (pp20) cc_final: 0.8437 (pp20) REVERT: C 324 GLN cc_start: 0.9134 (mt0) cc_final: 0.8869 (mm110) REVERT: C 352 ASP cc_start: 0.8567 (p0) cc_final: 0.8202 (p0) REVERT: D 130 GLU cc_start: 0.9000 (tt0) cc_final: 0.8300 (tm-30) REVERT: D 190 SER cc_start: 0.9000 (t) cc_final: 0.8603 (p) REVERT: D 356 ASP cc_start: 0.8764 (m-30) cc_final: 0.8426 (m-30) REVERT: E 101 ASN cc_start: 0.8383 (m-40) cc_final: 0.7868 (t0) REVERT: E 170 ASP cc_start: 0.8667 (m-30) cc_final: 0.8175 (t0) REVERT: E 363 MET cc_start: 0.8716 (mmt) cc_final: 0.8405 (tpp) REVERT: E 377 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8356 (mm-30) REVERT: F 216 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7913 (tm-30) REVERT: F 247 CYS cc_start: 0.9200 (m) cc_final: 0.8954 (m) REVERT: F 261 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.8083 (ttp80) REVERT: F 303 GLU cc_start: 0.7557 (mp0) cc_final: 0.7356 (mp0) REVERT: F 324 GLN cc_start: 0.9356 (mt0) cc_final: 0.9075 (mm110) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.2300 time to fit residues: 83.1924 Evaluate side-chains 181 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 92 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.075831 restraints weight = 154990.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079563 restraints weight = 68749.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082010 restraints weight = 40996.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.083598 restraints weight = 29323.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084603 restraints weight = 23566.814| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16308 Z= 0.138 Angle : 0.492 6.098 22075 Z= 0.255 Chirality : 0.039 0.146 2599 Planarity : 0.003 0.027 2840 Dihedral : 10.705 179.307 2405 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.18), residues: 2047 helix: 0.42 (0.17), residues: 916 sheet: -0.23 (0.31), residues: 289 loop : -0.69 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 200 TYR 0.010 0.001 TYR F 96 PHE 0.009 0.001 PHE E 298 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (16307) covalent geometry : angle 0.49218 / 0.26 (22075) hydrogen bonds : bond 0.03087 / 2.13 ( 594) hydrogen bonds : angle 5.00453 / 3.50 ( 1671) Misc. bond : bond 0.00642 / 0.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8148 (t80) cc_final: 0.7931 (t80) REVERT: A 317 LEU cc_start: 0.7132 (mt) cc_final: 0.6915 (mt) REVERT: A 384 MET cc_start: 0.8535 (mpp) cc_final: 0.8303 (mpp) REVERT: B 188 LYS cc_start: 0.8615 (tttt) cc_final: 0.8274 (tttm) REVERT: B 352 ASP cc_start: 0.8413 (p0) cc_final: 0.8083 (p0) REVERT: B 390 MET cc_start: 0.8672 (tpt) cc_final: 0.8379 (tpt) REVERT: C 320 GLU cc_start: 0.8782 (pp20) cc_final: 0.8459 (pp20) REVERT: C 324 GLN cc_start: 0.9185 (mt0) cc_final: 0.8927 (mm110) REVERT: C 352 ASP cc_start: 0.8581 (p0) cc_final: 0.8227 (p0) REVERT: D 130 GLU cc_start: 0.9040 (tt0) cc_final: 0.8430 (tm-30) REVERT: D 190 SER cc_start: 0.9102 (t) cc_final: 0.8725 (p) REVERT: D 356 ASP cc_start: 0.8800 (m-30) cc_final: 0.8452 (m-30) REVERT: E 135 LEU cc_start: 0.7888 (tt) cc_final: 0.7484 (tt) REVERT: E 170 ASP cc_start: 0.8803 (m-30) cc_final: 0.8269 (t0) REVERT: E 363 MET cc_start: 0.8686 (mmt) cc_final: 0.8411 (tpp) REVERT: E 413 TYR cc_start: 0.8321 (m-80) cc_final: 0.7707 (m-80) REVERT: F 182 TYR cc_start: 0.8698 (t80) cc_final: 0.8282 (t80) REVERT: F 216 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7906 (tm-30) REVERT: F 247 CYS cc_start: 0.9279 (m) cc_final: 0.9009 (m) REVERT: F 261 ARG cc_start: 0.8620 (ttt-90) cc_final: 0.8194 (ttp80) REVERT: F 303 GLU cc_start: 0.7567 (mp0) cc_final: 0.7314 (mp0) REVERT: F 324 GLN cc_start: 0.9356 (mt0) cc_final: 0.9088 (mm110) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2399 time to fit residues: 84.9072 Evaluate side-chains 179 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 146 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.099549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075471 restraints weight = 154048.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079144 restraints weight = 68261.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081597 restraints weight = 40754.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083167 restraints weight = 29052.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.084181 restraints weight = 23372.121| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16308 Z= 0.128 Angle : 0.478 6.111 22075 Z= 0.247 Chirality : 0.039 0.144 2599 Planarity : 0.003 0.028 2840 Dihedral : 10.531 179.922 2405 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.19), residues: 2047 helix: 0.52 (0.17), residues: 918 sheet: -0.08 (0.31), residues: 288 loop : -0.61 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 200 TYR 0.009 0.001 TYR A 93 PHE 0.008 0.001 PHE A 341 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16307) covalent geometry : angle 0.47822 / 0.25 (22075) hydrogen bonds : bond 0.02894 / 1.99 ( 594) hydrogen bonds : angle 4.90667 / 3.41 ( 1671) Misc. bond : bond 0.00633 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.7060 (mt) cc_final: 0.6848 (mt) REVERT: A 384 MET cc_start: 0.8573 (mpp) cc_final: 0.8202 (mpp) REVERT: B 150 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6673 (tm-30) REVERT: B 188 LYS cc_start: 0.8427 (tttt) cc_final: 0.8169 (tttm) REVERT: B 352 ASP cc_start: 0.8394 (p0) cc_final: 0.8078 (p0) REVERT: B 363 MET cc_start: 0.8538 (mtm) cc_final: 0.8323 (ptp) REVERT: C 320 GLU cc_start: 0.8799 (pp20) cc_final: 0.8478 (pp20) REVERT: C 324 GLN cc_start: 0.9229 (mt0) cc_final: 0.8992 (mm110) REVERT: C 352 ASP cc_start: 0.8540 (p0) cc_final: 0.8185 (p0) REVERT: D 94 ASN cc_start: 0.9288 (m-40) cc_final: 0.8988 (m-40) REVERT: D 130 GLU cc_start: 0.9067 (tt0) cc_final: 0.8433 (tm-30) REVERT: D 190 SER cc_start: 0.9172 (t) cc_final: 0.8775 (p) REVERT: D 356 ASP cc_start: 0.8754 (m-30) cc_final: 0.8415 (m-30) REVERT: E 170 ASP cc_start: 0.8774 (m-30) cc_final: 0.8254 (t0) REVERT: E 363 MET cc_start: 0.8663 (mmt) cc_final: 0.8385 (tpp) REVERT: E 413 TYR cc_start: 0.8345 (m-80) cc_final: 0.7765 (m-80) REVERT: F 182 TYR cc_start: 0.8741 (t80) cc_final: 0.8279 (t80) REVERT: F 216 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7949 (tm-30) REVERT: F 247 CYS cc_start: 0.9254 (m) cc_final: 0.9001 (m) REVERT: F 261 ARG cc_start: 0.8706 (ttt-90) cc_final: 0.8172 (ttp80) REVERT: F 303 GLU cc_start: 0.7665 (mp0) cc_final: 0.7401 (mp0) REVERT: F 324 GLN cc_start: 0.9340 (mt0) cc_final: 0.9081 (mm110) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2543 time to fit residues: 89.8743 Evaluate side-chains 179 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 113 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074216 restraints weight = 154033.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077830 restraints weight = 68149.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080220 restraints weight = 40619.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.081779 restraints weight = 29040.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082733 restraints weight = 23393.421| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16308 Z= 0.127 Angle : 0.480 6.773 22075 Z= 0.248 Chirality : 0.039 0.144 2599 Planarity : 0.003 0.029 2840 Dihedral : 10.419 178.426 2405 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2047 helix: 0.56 (0.17), residues: 924 sheet: 0.14 (0.30), residues: 298 loop : -0.62 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 200 TYR 0.009 0.001 TYR F 96 PHE 0.007 0.001 PHE A 341 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16307) covalent geometry : angle 0.48031 / 0.25 (22075) hydrogen bonds : bond 0.02796 / 1.92 ( 594) hydrogen bonds : angle 4.87105 / 3.39 ( 1671) Misc. bond : bond 0.00645 / 0.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LEU cc_start: 0.6934 (mt) cc_final: 0.6710 (mt) REVERT: A 384 MET cc_start: 0.8631 (mpp) cc_final: 0.8210 (mpp) REVERT: B 188 LYS cc_start: 0.8432 (tttt) cc_final: 0.8172 (tttm) REVERT: B 352 ASP cc_start: 0.8381 (p0) cc_final: 0.8076 (p0) REVERT: C 320 GLU cc_start: 0.8730 (pp20) cc_final: 0.8428 (pp20) REVERT: C 352 ASP cc_start: 0.8501 (p0) cc_final: 0.8157 (p0) REVERT: D 94 ASN cc_start: 0.9253 (m-40) cc_final: 0.8890 (m-40) REVERT: D 130 GLU cc_start: 0.9078 (tt0) cc_final: 0.8439 (tm-30) REVERT: D 190 SER cc_start: 0.9236 (t) cc_final: 0.8795 (p) REVERT: D 356 ASP cc_start: 0.8756 (m-30) cc_final: 0.8424 (m-30) REVERT: E 96 TYR cc_start: 0.8798 (m-80) cc_final: 0.8583 (m-10) REVERT: E 135 LEU cc_start: 0.8014 (tt) cc_final: 0.7410 (tt) REVERT: E 170 ASP cc_start: 0.8787 (m-30) cc_final: 0.8250 (t0) REVERT: E 363 MET cc_start: 0.8647 (mmt) cc_final: 0.8378 (tpp) REVERT: E 413 TYR cc_start: 0.8356 (m-80) cc_final: 0.7788 (m-80) REVERT: F 182 TYR cc_start: 0.8846 (t80) cc_final: 0.8383 (t80) REVERT: F 216 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 247 CYS cc_start: 0.9233 (m) cc_final: 0.8993 (m) REVERT: F 261 ARG cc_start: 0.8695 (ttt-90) cc_final: 0.8153 (ttp80) REVERT: F 303 GLU cc_start: 0.7699 (mp0) cc_final: 0.7416 (mp0) REVERT: F 324 GLN cc_start: 0.9323 (mt0) cc_final: 0.9081 (mm110) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2583 time to fit residues: 87.2844 Evaluate side-chains 180 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 101 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.095027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.071399 restraints weight = 154843.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074901 restraints weight = 69494.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077213 restraints weight = 41817.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078679 restraints weight = 30095.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079621 restraints weight = 24448.267| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16308 Z= 0.221 Angle : 0.576 6.148 22075 Z= 0.304 Chirality : 0.040 0.150 2599 Planarity : 0.003 0.046 2840 Dihedral : 10.533 176.817 2405 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.18), residues: 2047 helix: 0.11 (0.17), residues: 920 sheet: -0.09 (0.30), residues: 305 loop : -0.81 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 307 TYR 0.012 0.002 TYR A 96 PHE 0.013 0.002 PHE E 298 HIS 0.010 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (16307) covalent geometry : angle 0.57587 / 0.30 (22075) hydrogen bonds : bond 0.03346 / 2.30 ( 594) hydrogen bonds : angle 5.36265 / 3.72 ( 1671) Misc. bond : bond 0.00752 / 0.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 LYS cc_start: 0.8508 (tttt) cc_final: 0.8261 (tttm) REVERT: B 352 ASP cc_start: 0.8457 (p0) cc_final: 0.8180 (p0) REVERT: C 320 GLU cc_start: 0.8778 (pp20) cc_final: 0.8495 (pp20) REVERT: C 352 ASP cc_start: 0.8555 (p0) cc_final: 0.8232 (p0) REVERT: D 94 ASN cc_start: 0.9286 (m-40) cc_final: 0.8992 (m-40) REVERT: D 130 GLU cc_start: 0.9191 (tt0) cc_final: 0.8642 (tm-30) REVERT: D 205 GLU cc_start: 0.8291 (tt0) cc_final: 0.8070 (tt0) REVERT: D 356 ASP cc_start: 0.8880 (m-30) cc_final: 0.8535 (m-30) REVERT: E 135 LEU cc_start: 0.8309 (tt) cc_final: 0.7967 (tt) REVERT: E 170 ASP cc_start: 0.8906 (m-30) cc_final: 0.8314 (t70) REVERT: E 205 GLU cc_start: 0.8923 (tt0) cc_final: 0.8320 (tm-30) REVERT: E 363 MET cc_start: 0.8708 (mmt) cc_final: 0.8464 (tpp) REVERT: E 413 TYR cc_start: 0.8326 (m-80) cc_final: 0.7805 (m-80) REVERT: F 182 TYR cc_start: 0.8853 (t80) cc_final: 0.8487 (t80) REVERT: F 261 ARG cc_start: 0.8629 (ttt-90) cc_final: 0.8104 (ttp80) REVERT: F 303 GLU cc_start: 0.7725 (mp0) cc_final: 0.7450 (mp0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2607 time to fit residues: 84.6403 Evaluate side-chains 169 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 107 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 18 optimal weight: 0.0060 chunk 170 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074234 restraints weight = 152408.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077894 restraints weight = 67228.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080288 restraints weight = 39801.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081849 restraints weight = 28547.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082705 restraints weight = 23020.883| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16308 Z= 0.091 Angle : 0.478 6.047 22075 Z= 0.245 Chirality : 0.040 0.150 2599 Planarity : 0.003 0.045 2840 Dihedral : 10.427 178.799 2405 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.19), residues: 2047 helix: 0.67 (0.17), residues: 922 sheet: 0.13 (0.30), residues: 295 loop : -0.56 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 307 TYR 0.010 0.001 TYR E 96 PHE 0.015 0.001 PHE A 245 HIS 0.011 0.001 HIS F 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (16307) covalent geometry : angle 0.47759 / 0.25 (22075) hydrogen bonds : bond 0.02763 / 1.89 ( 594) hydrogen bonds : angle 4.71383 / 3.29 ( 1671) Misc. bond : bond 0.00570 / 0.38 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 TYR cc_start: 0.8821 (m-10) cc_final: 0.8435 (m-10) REVERT: B 150 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6799 (tm-30) REVERT: B 188 LYS cc_start: 0.8461 (tttt) cc_final: 0.8203 (tttm) REVERT: B 352 ASP cc_start: 0.8398 (p0) cc_final: 0.8114 (p0) REVERT: C 352 ASP cc_start: 0.8491 (p0) cc_final: 0.8148 (p0) REVERT: D 94 ASN cc_start: 0.9269 (m-40) cc_final: 0.8878 (m-40) REVERT: D 130 GLU cc_start: 0.9088 (tt0) cc_final: 0.8554 (tm-30) REVERT: D 205 GLU cc_start: 0.8039 (tt0) cc_final: 0.7823 (tt0) REVERT: D 356 ASP cc_start: 0.8763 (m-30) cc_final: 0.8404 (m-30) REVERT: E 93 TYR cc_start: 0.8598 (t80) cc_final: 0.8340 (t80) REVERT: E 144 ASP cc_start: 0.8229 (p0) cc_final: 0.8013 (p0) REVERT: E 170 ASP cc_start: 0.8754 (m-30) cc_final: 0.8194 (t70) REVERT: E 363 MET cc_start: 0.8724 (mmt) cc_final: 0.8479 (tpp) REVERT: E 413 TYR cc_start: 0.8258 (m-80) cc_final: 0.7760 (m-80) REVERT: F 182 TYR cc_start: 0.8886 (t80) cc_final: 0.8383 (t80) REVERT: F 216 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8257 (tm-30) REVERT: F 261 ARG cc_start: 0.8674 (ttt-90) cc_final: 0.8102 (ttp80) REVERT: F 303 GLU cc_start: 0.7765 (mp0) cc_final: 0.7437 (mp0) REVERT: F 324 GLN cc_start: 0.9315 (mt0) cc_final: 0.9087 (mm110) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2551 time to fit residues: 86.1367 Evaluate side-chains 169 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 100 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.095881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072252 restraints weight = 154151.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075738 restraints weight = 68313.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078055 restraints weight = 41045.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079543 restraints weight = 29605.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.080532 restraints weight = 24015.895| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16308 Z= 0.162 Angle : 0.515 6.098 22075 Z= 0.269 Chirality : 0.039 0.140 2599 Planarity : 0.003 0.037 2840 Dihedral : 10.372 176.757 2405 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.19), residues: 2047 helix: 0.51 (0.17), residues: 926 sheet: 0.26 (0.30), residues: 298 loop : -0.70 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.015 0.001 TYR E 96 PHE 0.012 0.001 PHE A 245 HIS 0.009 0.001 HIS F 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (16307) covalent geometry : angle 0.51528 / 0.27 (22075) hydrogen bonds : bond 0.02905 / 2.00 ( 594) hydrogen bonds : angle 4.98688 / 3.46 ( 1671) Misc. bond : bond 0.00697 / 0.46 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4692.30 seconds wall clock time: 80 minutes 47.85 seconds (4847.85 seconds total)