Starting phenix.real_space_refine on Fri Feb 6 03:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.map" model { file = "/net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irf_60812/02_2026/9irf_60812.cif" } resolution = 2.8 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 45 5.16 5 C 13754 2.51 5 N 3933 2.21 5 O 4381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22171 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2329 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Chain: "B" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1438 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2559 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain: "D" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2559 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain: "E" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2566 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain: "G" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2542 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain: "H" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2340 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 290} Chain breaks: 1 Chain: "I" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1244 Classifications: {'DNA': 1, 'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 14} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2028 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain breaks: 3 Time building chain proxies: 4.48, per 1000 atoms: 0.20 Number of scatterers: 22171 At special positions: 0 Unit cell: (120, 149.25, 158.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 58 15.00 O 4381 8.00 N 3933 7.00 C 13754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 921.4 milliseconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 43 sheets defined 39.2% alpha, 20.7% beta 5 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 27 through 46 removed outlier: 4.074A pdb=" N PHE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 148 through 158 removed outlier: 4.358A pdb=" N ARG A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.587A pdb=" N LEU A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 4.027A pdb=" N ALA A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.773A pdb=" N LEU A 279 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 35 removed outlier: 3.735A pdb=" N LEU B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.936A pdb=" N VAL B 132 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 133 " --> pdb=" O ASP B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.846A pdb=" N SER C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.643A pdb=" N LEU C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.798A pdb=" N GLY C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 removed outlier: 6.606A pdb=" N ARG C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.675A pdb=" N ARG C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 236' Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 269 through 274 removed outlier: 4.314A pdb=" N ALA C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.507A pdb=" N THR D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.532A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.703A pdb=" N GLY D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 removed outlier: 6.611A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.526A pdb=" N ILE D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 removed outlier: 4.085A pdb=" N ALA D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.525A pdb=" N LEU E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.845A pdb=" N GLY E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 153 removed outlier: 6.556A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.525A pdb=" N ALA E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.789A pdb=" N ARG E 235 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 236' Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 269 through 274 removed outlier: 4.160A pdb=" N ALA E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 299 through 309 Processing helix chain 'E' and resid 315 through 329 Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.699A pdb=" N THR F 61 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.726A pdb=" N LYS F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 145 removed outlier: 3.718A pdb=" N GLY F 145 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 removed outlier: 6.360A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 187 through 201 removed outlier: 3.519A pdb=" N ALA F 191 " --> pdb=" O GLY F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.960A pdb=" N ARG F 235 " --> pdb=" O ASP F 231 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 236' Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.509A pdb=" N ILE F 256 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 removed outlier: 4.392A pdb=" N ALA F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 309 Processing helix chain 'F' and resid 315 through 329 Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.742A pdb=" N ASP G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 145 through 153 removed outlier: 6.440A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'G' and resid 231 through 236 removed outlier: 3.838A pdb=" N ASN G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.532A pdb=" N ILE G 256 " --> pdb=" O HIS G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 274 removed outlier: 3.922A pdb=" N ALA G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 309 Processing helix chain 'G' and resid 315 through 329 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 153 removed outlier: 6.052A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'H' and resid 252 through 261 removed outlier: 3.564A pdb=" N ILE H 256 " --> pdb=" O HIS H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 274 removed outlier: 4.469A pdb=" N ALA H 273 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 Processing helix chain 'H' and resid 299 through 309 Processing helix chain 'H' and resid 315 through 329 Processing helix chain 'J' and resid 191 through 193 No H-bonds generated for 'chain 'J' and resid 191 through 193' Processing helix chain 'J' and resid 205 through 220 removed outlier: 3.597A pdb=" N GLY J 220 " --> pdb=" O ALA J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 232 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.519A pdb=" N ILE J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 267 Processing helix chain 'J' and resid 304 through 318 removed outlier: 3.816A pdb=" N GLN J 310 " --> pdb=" O ALA J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 351 Processing helix chain 'J' and resid 355 through 359 removed outlier: 3.549A pdb=" N ALA J 358 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU J 359 " --> pdb=" O TRP J 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 355 through 359' Processing helix chain 'J' and resid 363 through 371 removed outlier: 4.125A pdb=" N LEU J 368 " --> pdb=" O ARG J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 377 Processing helix chain 'J' and resid 378 through 388 removed outlier: 3.700A pdb=" N GLY J 388 " --> pdb=" O GLU J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 406 Processing helix chain 'J' and resid 414 through 422 Processing helix chain 'J' and resid 424 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 6.556A pdb=" N MET A 97 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU A 13 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 9 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 99 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 100 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 55 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 102 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS A 53 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 14.405A pdb=" N CYS A 53 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ASP A 167 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 55 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 165 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE A 256 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA A 234 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 258 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 260 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 230 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.576A pdb=" N GLU A 13 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN A 11 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 137 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG A 9 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG A 139 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 7 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 141 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 5 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN A 143 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR A 3 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 9 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 99 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 100 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 55 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 102 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS A 53 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 14.405A pdb=" N CYS A 53 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ASP A 167 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 55 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 165 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER J 199 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 257 " --> pdb=" O SER J 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 144 removed outlier: 4.558A pdb=" N PHE B 155 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 100 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 93 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 30 current: chain 'C' and resid 157 through 164 removed outlier: 3.846A pdb=" N LYS C 164 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 99 current: chain 'C' and resid 244 through 245 Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 49 Processing sheet with id=AB3, first strand: chain 'C' and resid 262 through 264 Processing sheet with id=AB4, first strand: chain 'C' and resid 283 through 284 Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.660A pdb=" N VAL D 108 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 30 current: chain 'D' and resid 158 through 164 removed outlier: 3.789A pdb=" N LYS D 164 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.945A pdb=" N ASN D 75 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER D 239 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS D 78 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=AC1, first strand: chain 'D' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.607A pdb=" N VAL E 108 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 30 current: chain 'E' and resid 157 through 164 removed outlier: 3.878A pdb=" N LYS E 164 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 40 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 99 current: chain 'E' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'E' and resid 44 through 50 Processing sheet with id=AC6, first strand: chain 'E' and resid 262 through 264 Processing sheet with id=AC7, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AC8, first strand: chain 'F' and resid 108 through 109 removed outlier: 4.161A pdb=" N VAL F 108 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 30 current: chain 'F' and resid 158 through 164 removed outlier: 3.722A pdb=" N LYS F 164 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 39 through 40 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 90 through 99 current: chain 'F' and resid 244 through 245 Processing sheet with id=AD2, first strand: chain 'F' and resid 44 through 50 removed outlier: 7.916A pdb=" N SER F 239 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS F 78 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 262 through 264 Processing sheet with id=AD4, first strand: chain 'F' and resid 283 through 284 Processing sheet with id=AD5, first strand: chain 'G' and resid 14 through 15 removed outlier: 3.909A pdb=" N ALA G 15 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL G 108 " --> pdb=" O ALA G 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 30 current: chain 'G' and resid 157 through 164 removed outlier: 3.803A pdb=" N LYS G 164 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG G 168 " --> pdb=" O LYS G 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 39 through 40 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 99 current: chain 'G' and resid 244 through 245 Processing sheet with id=AD8, first strand: chain 'G' and resid 44 through 50 removed outlier: 7.957A pdb=" N SER G 239 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LYS G 78 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 283 through 284 removed outlier: 3.976A pdb=" N LYS G 289 " --> pdb=" O VAL G 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 15 through 16 Processing sheet with id=AE2, first strand: chain 'H' and resid 20 through 22 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 30 current: chain 'H' and resid 158 through 164 Processing sheet with id=AE3, first strand: chain 'H' and resid 39 through 40 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 99 current: chain 'H' and resid 244 through 245 Processing sheet with id=AE4, first strand: chain 'H' and resid 44 through 46 Processing sheet with id=AE5, first strand: chain 'H' and resid 262 through 264 Processing sheet with id=AE6, first strand: chain 'H' and resid 283 through 284 removed outlier: 3.605A pdb=" N LYS H 289 " --> pdb=" O VAL H 284 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 247 through 250 removed outlier: 3.615A pdb=" N ALA J 247 " --> pdb=" O LEU J 272 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3660 1.25 - 1.40: 5617 1.40 - 1.54: 12902 1.54 - 1.68: 470 1.68 - 1.82: 76 Bond restraints: 22725 Sorted by residual: bond pdb=" CA TYR J 302 " pdb=" C TYR J 302 " ideal model delta sigma weight residual 1.525 1.156 0.369 2.10e-02 2.27e+03 3.09e+02 bond pdb=" N TYR J 302 " pdb=" CA TYR J 302 " ideal model delta sigma weight residual 1.458 1.159 0.299 1.90e-02 2.77e+03 2.48e+02 bond pdb=" O3' C I 40 " pdb=" P G I 41 " ideal model delta sigma weight residual 1.607 1.460 0.147 1.50e-02 4.44e+03 9.57e+01 bond pdb=" CA TYR J 302 " pdb=" CB TYR J 302 " ideal model delta sigma weight residual 1.530 1.351 0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" CB TYR J 302 " pdb=" CG TYR J 302 " ideal model delta sigma weight residual 1.512 1.344 0.168 2.20e-02 2.07e+03 5.84e+01 ... (remaining 22720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 30998 5.96 - 11.92: 71 11.92 - 17.89: 10 17.89 - 23.85: 2 23.85 - 29.81: 3 Bond angle restraints: 31084 Sorted by residual: angle pdb=" C TYR J 302 " pdb=" N HIS J 303 " pdb=" CA HIS J 303 " ideal model delta sigma weight residual 121.66 91.85 29.81 1.76e+00 3.23e-01 2.87e+02 angle pdb=" CA PRO G 294 " pdb=" N PRO G 294 " pdb=" CD PRO G 294 " ideal model delta sigma weight residual 112.00 94.03 17.97 1.40e+00 5.10e-01 1.65e+02 angle pdb=" O3' G I 41 " pdb=" C3' G I 41 " pdb=" C2' G I 41 " ideal model delta sigma weight residual 113.70 96.80 16.90 1.50e+00 4.44e-01 1.27e+02 angle pdb=" C4' G I 41 " pdb=" C3' G I 41 " pdb=" O3' G I 41 " ideal model delta sigma weight residual 113.00 129.77 -16.77 1.50e+00 4.44e-01 1.25e+02 angle pdb=" OP1 C I 46 " pdb=" P C I 46 " pdb=" O5' C I 46 " ideal model delta sigma weight residual 108.00 79.90 28.10 3.00e+00 1.11e-01 8.78e+01 ... (remaining 31079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 11894 20.01 - 40.02: 1305 40.02 - 60.03: 370 60.03 - 80.04: 89 80.04 - 100.05: 14 Dihedral angle restraints: 13672 sinusoidal: 5958 harmonic: 7714 Sorted by residual: dihedral pdb=" C TYR J 302 " pdb=" N TYR J 302 " pdb=" CA TYR J 302 " pdb=" CB TYR J 302 " ideal model delta harmonic sigma weight residual -122.60 -100.04 -22.56 0 2.50e+00 1.60e-01 8.15e+01 dihedral pdb=" N TYR J 302 " pdb=" C TYR J 302 " pdb=" CA TYR J 302 " pdb=" CB TYR J 302 " ideal model delta harmonic sigma weight residual 122.80 101.06 21.74 0 2.50e+00 1.60e-01 7.56e+01 dihedral pdb=" CA SER J 204 " pdb=" C SER J 204 " pdb=" N SER J 205 " pdb=" CA SER J 205 " ideal model delta harmonic sigma weight residual 180.00 145.60 34.40 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 13669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 3444 0.152 - 0.304: 19 0.304 - 0.456: 2 0.456 - 0.608: 1 0.608 - 0.760: 1 Chirality restraints: 3467 Sorted by residual: chirality pdb=" CA TYR J 302 " pdb=" N TYR J 302 " pdb=" C TYR J 302 " pdb=" CB TYR J 302 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" P C I 46 " pdb=" OP1 C I 46 " pdb=" OP2 C I 46 " pdb=" O5' C I 46 " both_signs ideal model delta sigma weight residual True 2.41 1.95 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C2' C I 46 " pdb=" C3' C I 46 " pdb=" O2' C I 46 " pdb=" C1' C I 46 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 3464 not shown) Planarity restraints: 3863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 293 " 0.080 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO G 294 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO G 294 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO G 294 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G I 41 " -0.016 2.00e-02 2.50e+03 2.26e-02 1.53e+01 pdb=" N9 G I 41 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G I 41 " -0.026 2.00e-02 2.50e+03 pdb=" N7 G I 41 " -0.015 2.00e-02 2.50e+03 pdb=" C5 G I 41 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G I 41 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G I 41 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G I 41 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G I 41 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G I 41 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G I 41 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G I 41 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 313 " 0.064 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO H 314 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO H 314 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 314 " 0.051 5.00e-02 4.00e+02 ... (remaining 3860 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 201 2.61 - 3.18: 17895 3.18 - 3.75: 32517 3.75 - 4.33: 45309 4.33 - 4.90: 75837 Nonbonded interactions: 171759 Sorted by model distance: nonbonded pdb=" N TYR J 302 " pdb=" N HIS J 303 " model vdw 2.033 2.560 nonbonded pdb=" O2' G I 51 " pdb=" N6 A I 55 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP A 190 " pdb=" NH1 ARG J 213 " model vdw 2.175 3.120 nonbonded pdb=" OE2 GLU A 258 " pdb=" OG1 THR J 78 " model vdw 2.178 3.040 nonbonded pdb=" NH2 ARG G 261 " pdb=" OP2 A I 8 " model vdw 2.184 3.120 ... (remaining 171754 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 'C' and (resid 10 through 47 or resid 77 through 337)) selection = (chain 'D' and (resid 10 through 47 or resid 77 through 337)) selection = (chain 'E' and (resid 10 through 47 or resid 77 through 337)) selection = (chain 'F' and (resid 10 through 47 or resid 77 through 337)) selection = (chain 'G' and (resid 10 through 47 or resid 77 through 337)) selection = (chain 'H' and resid 10 through 337) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.000 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.006 0.369 22725 Z= 0.285 Angle : 0.865 29.809 31084 Z= 0.454 Chirality : 0.048 0.760 3467 Planarity : 0.006 0.107 3863 Dihedral : 18.252 100.054 8716 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 2.41 % Allowed : 25.73 % Favored : 71.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2651 helix: 1.72 (0.18), residues: 798 sheet: 1.73 (0.25), residues: 458 loop : -0.80 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 139 TYR 0.014 0.001 TYR J 302 PHE 0.054 0.002 PHE J 343 TRP 0.017 0.001 TRP A 69 HIS 0.011 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00569 (22725) covalent geometry : angle 0.86471 (31084) hydrogen bonds : bond 0.15943 ( 863) hydrogen bonds : angle 5.88621 ( 2443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 469 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7618 (mm) cc_final: 0.7284 (tp) REVERT: A 133 THR cc_start: 0.8034 (m) cc_final: 0.7740 (p) REVERT: C 184 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 271 ASP cc_start: 0.8486 (m-30) cc_final: 0.8271 (m-30) REVERT: D 20 LEU cc_start: 0.8729 (mt) cc_final: 0.8469 (mp) REVERT: D 58 ASN cc_start: 0.7835 (t0) cc_final: 0.7512 (t160) REVERT: D 163 THR cc_start: 0.8464 (t) cc_final: 0.8208 (m) REVERT: D 226 GLN cc_start: 0.8181 (tt0) cc_final: 0.7941 (mt0) REVERT: D 238 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7671 (mttp) REVERT: D 297 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8072 (mmmm) REVERT: E 49 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7930 (ttt180) REVERT: E 287 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7709 (mtp180) REVERT: F 227 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7950 (mm-30) REVERT: F 295 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7279 (ttm-80) REVERT: F 298 MET cc_start: 0.8372 (tpp) cc_final: 0.8096 (mmt) REVERT: G 90 THR cc_start: 0.8173 (m) cc_final: 0.7898 (m) REVERT: G 140 GLU cc_start: 0.7676 (tt0) cc_final: 0.7373 (tt0) REVERT: G 181 GLN cc_start: 0.7966 (mt0) cc_final: 0.7764 (mp10) REVERT: G 207 LEU cc_start: 0.8270 (tt) cc_final: 0.8012 (tp) REVERT: H 156 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7327 (mm-30) REVERT: H 238 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7823 (mtpp) REVERT: H 299 ASP cc_start: 0.7861 (p0) cc_final: 0.7566 (p0) outliers start: 52 outliers final: 32 residues processed: 506 average time/residue: 0.6770 time to fit residues: 383.6732 Evaluate side-chains 469 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 437 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain J residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 96 HIS ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN D 75 ASN D 244 GLN E 44 GLN F 77 GLN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 226 GLN H 34 GLN H 105 GLN H 110 ASN H 173 ASN H 215 GLN H 218 ASN H 226 GLN H 244 GLN H 246 ASN H 306 ASN ** H 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN J 337 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117082 restraints weight = 32117.042| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.62 r_work: 0.3335 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22725 Z= 0.213 Angle : 0.628 13.044 31084 Z= 0.327 Chirality : 0.045 0.201 3467 Planarity : 0.005 0.056 3863 Dihedral : 13.842 89.639 3867 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.71 % Allowed : 22.76 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.68 (0.16), residues: 2651 helix: 1.63 (0.18), residues: 848 sheet: 1.41 (0.25), residues: 474 loop : -0.70 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 139 TYR 0.014 0.002 TYR C 267 PHE 0.043 0.002 PHE J 343 TRP 0.014 0.001 TRP A 69 HIS 0.007 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00505 (22725) covalent geometry : angle 0.62843 (31084) hydrogen bonds : bond 0.05360 ( 863) hydrogen bonds : angle 4.66251 ( 2443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 452 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7740 (mm) cc_final: 0.7268 (tp) REVERT: A 98 THR cc_start: 0.7152 (t) cc_final: 0.6290 (m) REVERT: A 174 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6816 (ttp80) REVERT: C 44 GLN cc_start: 0.8318 (mm110) cc_final: 0.7998 (mm110) REVERT: C 75 ASN cc_start: 0.8035 (t0) cc_final: 0.7743 (t0) REVERT: C 184 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: D 24 ASP cc_start: 0.8371 (m-30) cc_final: 0.8162 (m-30) REVERT: D 58 ASN cc_start: 0.7548 (t0) cc_final: 0.7221 (t0) REVERT: E 43 ILE cc_start: 0.8838 (mm) cc_final: 0.8629 (mm) REVERT: E 49 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8323 (ttp-170) REVERT: E 287 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7835 (mtp85) REVERT: E 297 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8266 (mmmm) REVERT: F 51 THR cc_start: 0.8537 (p) cc_final: 0.8303 (m) REVERT: F 165 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7703 (tmmm) REVERT: F 218 ASN cc_start: 0.8659 (m110) cc_final: 0.8348 (m-40) REVERT: F 227 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8237 (mm-30) REVERT: F 279 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: F 287 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8499 (mtp85) REVERT: F 289 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: F 295 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7694 (mtt-85) REVERT: G 90 THR cc_start: 0.8235 (m) cc_final: 0.7974 (m) REVERT: G 127 GLN cc_start: 0.7756 (mm110) cc_final: 0.7501 (mm-40) REVERT: H 111 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7086 (t70) REVERT: H 156 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7835 (tm-30) REVERT: H 159 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8379 (ttt-90) REVERT: H 171 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7771 (mt-10) REVERT: H 238 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7673 (mtpp) REVERT: H 296 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: H 299 ASP cc_start: 0.7906 (p0) cc_final: 0.7705 (p0) REVERT: J 249 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6441 (tp-100) REVERT: J 251 MET cc_start: 0.5256 (mmt) cc_final: 0.4719 (mmt) REVERT: J 310 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: J 352 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6530 (tm) REVERT: J 404 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6838 (pmt-80) outliers start: 80 outliers final: 34 residues processed: 494 average time/residue: 0.6922 time to fit residues: 382.1693 Evaluate side-chains 481 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 436 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain J residue 310 GLN Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 188 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN E 129 GLN F 44 GLN G 35 GLN G 44 GLN H 34 GLN H 215 GLN H 306 ASN J 337 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118203 restraints weight = 32171.024| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.75 r_work: 0.3354 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22725 Z= 0.131 Angle : 0.546 11.944 31084 Z= 0.281 Chirality : 0.042 0.177 3467 Planarity : 0.004 0.043 3863 Dihedral : 13.518 87.266 3838 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.52 % Allowed : 22.67 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.92 (0.16), residues: 2651 helix: 1.91 (0.18), residues: 849 sheet: 1.56 (0.25), residues: 463 loop : -0.61 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 271 TYR 0.013 0.001 TYR G 321 PHE 0.022 0.001 PHE J 343 TRP 0.011 0.001 TRP A 69 HIS 0.005 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00298 (22725) covalent geometry : angle 0.54565 (31084) hydrogen bonds : bond 0.04235 ( 863) hydrogen bonds : angle 4.26512 ( 2443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 462 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7720 (mm) cc_final: 0.7229 (tp) REVERT: A 174 ARG cc_start: 0.7128 (ttp80) cc_final: 0.6719 (ttp80) REVERT: B 24 LEU cc_start: 0.9064 (tp) cc_final: 0.8748 (tm) REVERT: B 51 LEU cc_start: 0.8579 (tp) cc_final: 0.8202 (tt) REVERT: B 146 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7938 (tm) REVERT: C 44 GLN cc_start: 0.7994 (mm110) cc_final: 0.7771 (mm-40) REVERT: C 75 ASN cc_start: 0.7794 (t0) cc_final: 0.7537 (t0) REVERT: C 105 GLN cc_start: 0.8453 (tp40) cc_final: 0.8251 (tp-100) REVERT: C 184 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: C 238 LYS cc_start: 0.7885 (mttp) cc_final: 0.7631 (mttm) REVERT: C 240 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7868 (ttpp) REVERT: D 24 ASP cc_start: 0.8098 (m-30) cc_final: 0.7889 (m-30) REVERT: D 58 ASN cc_start: 0.7441 (t0) cc_final: 0.7127 (t0) REVERT: D 127 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: D 238 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7420 (mttt) REVERT: E 13 VAL cc_start: 0.8489 (t) cc_final: 0.8207 (m) REVERT: E 49 ARG cc_start: 0.8310 (ttt180) cc_final: 0.8068 (ttp-170) REVERT: E 297 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8114 (mmmm) REVERT: F 51 THR cc_start: 0.8421 (p) cc_final: 0.8179 (m) REVERT: F 165 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7578 (tmmm) REVERT: F 218 ASN cc_start: 0.8494 (m110) cc_final: 0.8191 (m-40) REVERT: F 289 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8235 (mtmm) REVERT: F 295 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7474 (mtt-85) REVERT: G 90 THR cc_start: 0.8002 (m) cc_final: 0.7594 (m) REVERT: G 123 THR cc_start: 0.8151 (t) cc_final: 0.7877 (m) REVERT: G 193 THR cc_start: 0.8628 (m) cc_final: 0.8390 (m) REVERT: G 228 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7250 (mt) REVERT: H 156 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7584 (tm-30) REVERT: H 198 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8341 (mmmm) REVERT: H 238 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7669 (mtpp) REVERT: H 296 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: J 251 MET cc_start: 0.5238 (mmt) cc_final: 0.4888 (mmt) REVERT: J 310 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6075 (pm20) REVERT: J 352 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6460 (tm) outliers start: 76 outliers final: 41 residues processed: 505 average time/residue: 0.7795 time to fit residues: 439.6426 Evaluate side-chains 496 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 445 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 269 ARG Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 310 GLN Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 173 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN E 44 GLN E 129 GLN F 77 GLN G 77 GLN H 115 GLN H 173 ASN H 215 GLN H 226 GLN H 306 ASN J 249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116613 restraints weight = 31976.974| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.69 r_work: 0.3344 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22725 Z= 0.169 Angle : 0.556 10.328 31084 Z= 0.287 Chirality : 0.043 0.213 3467 Planarity : 0.004 0.043 3863 Dihedral : 13.401 91.670 3833 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.54 % Allowed : 22.25 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.86 (0.16), residues: 2651 helix: 1.91 (0.17), residues: 850 sheet: 1.45 (0.25), residues: 464 loop : -0.66 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 271 TYR 0.020 0.001 TYR G 321 PHE 0.012 0.002 PHE G 95 TRP 0.012 0.001 TRP A 69 HIS 0.004 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00397 (22725) covalent geometry : angle 0.55576 (31084) hydrogen bonds : bond 0.04660 ( 863) hydrogen bonds : angle 4.24194 ( 2443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 457 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7752 (mm) cc_final: 0.7367 (mt) REVERT: A 123 GLN cc_start: 0.8136 (mt0) cc_final: 0.7610 (mt0) REVERT: A 189 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7870 (pp) REVERT: B 51 LEU cc_start: 0.8688 (tp) cc_final: 0.8323 (tt) REVERT: B 146 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7981 (tm) REVERT: B 183 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.6509 (t-100) REVERT: C 75 ASN cc_start: 0.8039 (t0) cc_final: 0.7822 (t0) REVERT: C 184 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: C 238 LYS cc_start: 0.8098 (mttp) cc_final: 0.7828 (mttm) REVERT: C 240 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8087 (ttpp) REVERT: D 24 ASP cc_start: 0.8317 (m-30) cc_final: 0.8109 (m-30) REVERT: D 58 ASN cc_start: 0.7355 (t0) cc_final: 0.7080 (t0) REVERT: D 127 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: D 238 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7783 (mttp) REVERT: E 13 VAL cc_start: 0.8633 (t) cc_final: 0.8373 (m) REVERT: E 49 ARG cc_start: 0.8537 (ttt180) cc_final: 0.8271 (ttp-170) REVERT: E 295 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7813 (mmm160) REVERT: E 297 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8275 (mmmm) REVERT: F 218 ASN cc_start: 0.8638 (m110) cc_final: 0.8408 (m110) REVERT: F 227 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8217 (mm-30) REVERT: F 287 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8508 (mtp85) REVERT: F 289 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: F 295 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7710 (mtt-85) REVERT: G 75 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8004 (p0) REVERT: G 90 THR cc_start: 0.8203 (m) cc_final: 0.7921 (m) REVERT: G 123 THR cc_start: 0.8263 (t) cc_final: 0.7965 (m) REVERT: G 193 THR cc_start: 0.8713 (m) cc_final: 0.8485 (m) REVERT: G 227 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7988 (mm-30) REVERT: G 228 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7466 (mt) REVERT: G 297 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7726 (tmmm) REVERT: H 156 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7915 (tm-30) REVERT: H 197 GLU cc_start: 0.7859 (tp30) cc_final: 0.7621 (tp30) REVERT: H 198 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8453 (mmmm) REVERT: H 238 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7725 (mtpp) REVERT: H 296 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: J 249 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6484 (tp-100) REVERT: J 251 MET cc_start: 0.5499 (mmt) cc_final: 0.4908 (mmt) REVERT: J 352 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6483 (tm) outliers start: 98 outliers final: 46 residues processed: 507 average time/residue: 0.7528 time to fit residues: 426.3067 Evaluate side-chains 511 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 451 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 338 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 196 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 240 optimal weight: 0.0870 chunk 148 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 129 GLN E 44 GLN E 129 GLN F 77 GLN H 215 GLN H 226 GLN H 258 ASN H 306 ASN J 249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.156877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118308 restraints weight = 31701.757| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.66 r_work: 0.3377 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22725 Z= 0.110 Angle : 0.521 11.393 31084 Z= 0.265 Chirality : 0.041 0.172 3467 Planarity : 0.004 0.043 3863 Dihedral : 13.248 92.963 3833 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.38 % Allowed : 23.50 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.04 (0.16), residues: 2651 helix: 2.12 (0.18), residues: 852 sheet: 1.42 (0.25), residues: 472 loop : -0.55 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 174 TYR 0.019 0.001 TYR G 321 PHE 0.010 0.001 PHE E 95 TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS J 333 Details of bonding type rmsd covalent geometry : bond 0.00248 (22725) covalent geometry : angle 0.52141 (31084) hydrogen bonds : bond 0.03753 ( 863) hydrogen bonds : angle 3.97830 ( 2443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 451 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7718 (mm) cc_final: 0.7325 (mt) REVERT: A 123 GLN cc_start: 0.8089 (mt0) cc_final: 0.7560 (mt0) REVERT: A 189 ILE cc_start: 0.8184 (tp) cc_final: 0.7838 (pp) REVERT: B 51 LEU cc_start: 0.8667 (tp) cc_final: 0.8293 (tt) REVERT: B 146 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7975 (tm) REVERT: C 184 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 240 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8013 (ttpp) REVERT: D 24 ASP cc_start: 0.8298 (m-30) cc_final: 0.8091 (m-30) REVERT: D 121 ILE cc_start: 0.8594 (mp) cc_final: 0.8175 (mp) REVERT: D 127 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: E 13 VAL cc_start: 0.8619 (t) cc_final: 0.8357 (m) REVERT: E 49 ARG cc_start: 0.8502 (ttt180) cc_final: 0.8233 (ttp-170) REVERT: E 120 ASP cc_start: 0.8149 (m-30) cc_final: 0.7915 (m-30) REVERT: E 295 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7832 (mmm160) REVERT: E 297 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8240 (mmmm) REVERT: F 45 GLU cc_start: 0.8184 (tt0) cc_final: 0.7951 (tt0) REVERT: F 51 THR cc_start: 0.8597 (p) cc_final: 0.8350 (m) REVERT: F 218 ASN cc_start: 0.8627 (m110) cc_final: 0.8415 (m-40) REVERT: F 238 LYS cc_start: 0.7979 (mttt) cc_final: 0.7675 (mttt) REVERT: F 289 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8379 (mtmm) REVERT: F 295 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.7691 (mtt-85) REVERT: G 75 ASN cc_start: 0.8274 (m110) cc_final: 0.8015 (p0) REVERT: G 90 THR cc_start: 0.8106 (m) cc_final: 0.7837 (m) REVERT: G 123 THR cc_start: 0.8211 (t) cc_final: 0.7997 (m) REVERT: G 197 GLU cc_start: 0.8173 (tp30) cc_final: 0.7891 (mm-30) REVERT: G 227 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7822 (mm-30) REVERT: G 228 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7386 (mt) REVERT: G 297 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7757 (tmmm) REVERT: H 111 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7126 (t70) REVERT: H 156 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7940 (tm-30) REVERT: H 159 ARG cc_start: 0.8665 (ttt-90) cc_final: 0.8380 (ttt-90) REVERT: H 171 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7728 (mt-10) REVERT: H 197 GLU cc_start: 0.7851 (tp30) cc_final: 0.7607 (tp30) REVERT: H 238 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7737 (mtpp) REVERT: H 296 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: J 249 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6680 (tp-100) REVERT: J 251 MET cc_start: 0.5450 (mmt) cc_final: 0.4842 (mmt) REVERT: J 310 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: J 352 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6421 (tm) outliers start: 73 outliers final: 39 residues processed: 494 average time/residue: 0.7726 time to fit residues: 426.1201 Evaluate side-chains 496 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 445 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 310 GLN Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 35 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 70 optimal weight: 0.0040 chunk 67 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 3 HIS C 75 ASN C 105 GLN C 129 GLN E 44 GLN E 129 GLN E 218 ASN F 44 GLN F 77 GLN H 215 GLN H 226 GLN H 246 ASN J 249 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119076 restraints weight = 32513.796| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.72 r_work: 0.3368 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22725 Z= 0.125 Angle : 0.524 10.328 31084 Z= 0.267 Chirality : 0.041 0.194 3467 Planarity : 0.004 0.049 3863 Dihedral : 13.197 93.792 3824 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.80 % Allowed : 23.78 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.07 (0.16), residues: 2651 helix: 2.14 (0.18), residues: 855 sheet: 1.40 (0.25), residues: 473 loop : -0.53 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.027 0.001 TYR G 321 PHE 0.010 0.001 PHE E 95 TRP 0.008 0.001 TRP G 266 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00286 (22725) covalent geometry : angle 0.52418 (31084) hydrogen bonds : bond 0.03920 ( 863) hydrogen bonds : angle 3.96906 ( 2443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 455 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7718 (mm) cc_final: 0.7323 (mt) REVERT: A 171 LEU cc_start: 0.7802 (mm) cc_final: 0.7601 (mp) REVERT: A 174 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6820 (ttp80) REVERT: B 51 LEU cc_start: 0.8695 (tp) cc_final: 0.8311 (tt) REVERT: B 146 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7957 (tm) REVERT: B 183 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.6516 (t-100) REVERT: C 184 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: C 240 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8022 (ttpp) REVERT: D 24 ASP cc_start: 0.8293 (m-30) cc_final: 0.8093 (m-30) REVERT: D 121 ILE cc_start: 0.8585 (mp) cc_final: 0.8168 (mp) REVERT: D 127 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: E 13 VAL cc_start: 0.8628 (t) cc_final: 0.8373 (m) REVERT: E 75 ASN cc_start: 0.8113 (m-40) cc_final: 0.7897 (m-40) REVERT: E 295 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7832 (mmm160) REVERT: E 297 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8248 (mmmm) REVERT: F 45 GLU cc_start: 0.8199 (tt0) cc_final: 0.7970 (tt0) REVERT: F 218 ASN cc_start: 0.8643 (m110) cc_final: 0.8407 (m110) REVERT: F 287 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8563 (mtp85) REVERT: F 289 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (mtmm) REVERT: F 295 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7706 (mtt-85) REVERT: G 75 ASN cc_start: 0.8170 (m110) cc_final: 0.7956 (p0) REVERT: G 90 THR cc_start: 0.8103 (m) cc_final: 0.7849 (m) REVERT: G 123 THR cc_start: 0.8237 (t) cc_final: 0.8002 (m) REVERT: G 197 GLU cc_start: 0.8312 (tp30) cc_final: 0.7963 (mm-30) REVERT: G 227 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7796 (mm-30) REVERT: G 228 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7417 (mt) REVERT: G 297 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7854 (tmmm) REVERT: H 111 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7123 (t70) REVERT: H 156 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7932 (tm-30) REVERT: H 159 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8383 (ttt-90) REVERT: H 171 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7764 (mt-10) REVERT: H 197 GLU cc_start: 0.7900 (tp30) cc_final: 0.7656 (tp30) REVERT: H 238 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7749 (mtpp) REVERT: H 296 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: H 318 GLN cc_start: 0.7894 (mp10) cc_final: 0.7362 (mp10) REVERT: J 251 MET cc_start: 0.5354 (mmt) cc_final: 0.4757 (mmt) REVERT: J 404 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6445 (pmt-80) outliers start: 82 outliers final: 42 residues processed: 500 average time/residue: 0.7644 time to fit residues: 426.8312 Evaluate side-chains 503 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 449 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 102 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 201 optimal weight: 0.0020 chunk 74 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS C 75 ASN C 105 GLN C 129 GLN D 58 ASN D 77 GLN E 44 GLN E 129 GLN F 77 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 218 ASN H 226 GLN H 246 ASN H 254 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118703 restraints weight = 32407.292| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.55 r_work: 0.3366 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22725 Z= 0.158 Angle : 0.551 11.872 31084 Z= 0.280 Chirality : 0.042 0.208 3467 Planarity : 0.004 0.058 3863 Dihedral : 13.208 94.131 3824 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.94 % Allowed : 23.97 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.98 (0.16), residues: 2651 helix: 2.07 (0.17), residues: 855 sheet: 1.41 (0.25), residues: 463 loop : -0.59 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.013 0.001 TYR G 291 PHE 0.012 0.001 PHE G 95 TRP 0.012 0.001 TRP G 266 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00373 (22725) covalent geometry : angle 0.55083 (31084) hydrogen bonds : bond 0.04322 ( 863) hydrogen bonds : angle 4.05273 ( 2443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 460 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7726 (mm) cc_final: 0.7350 (mt) REVERT: A 174 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6781 (ttp80) REVERT: B 51 LEU cc_start: 0.8701 (tp) cc_final: 0.8346 (tt) REVERT: B 183 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6510 (t-100) REVERT: C 184 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 240 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8022 (ttpp) REVERT: D 24 ASP cc_start: 0.8290 (m-30) cc_final: 0.8083 (m-30) REVERT: D 121 ILE cc_start: 0.8577 (mp) cc_final: 0.8148 (mp) REVERT: D 127 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: D 238 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7627 (mttt) REVERT: E 13 VAL cc_start: 0.8633 (t) cc_final: 0.8382 (m) REVERT: E 120 ASP cc_start: 0.8135 (m-30) cc_final: 0.7934 (m-30) REVERT: E 295 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7788 (mmm160) REVERT: E 297 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8235 (mmmm) REVERT: F 17 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 218 ASN cc_start: 0.8639 (m110) cc_final: 0.8391 (m110) REVERT: F 287 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8519 (mtp85) REVERT: F 289 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: F 295 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.7674 (mtt-85) REVERT: G 75 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7960 (p0) REVERT: G 90 THR cc_start: 0.8136 (m) cc_final: 0.7885 (m) REVERT: G 123 THR cc_start: 0.8292 (t) cc_final: 0.7982 (m) REVERT: G 227 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7758 (mm-30) REVERT: G 228 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7450 (mt) REVERT: G 297 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7931 (tmmm) REVERT: H 156 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7885 (tm-30) REVERT: H 159 ARG cc_start: 0.8703 (ttt-90) cc_final: 0.8446 (ttt-90) REVERT: H 171 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7806 (mt-10) REVERT: H 197 GLU cc_start: 0.7867 (tp30) cc_final: 0.7601 (tp30) REVERT: H 198 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8423 (mmmm) REVERT: H 238 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7740 (mtpp) REVERT: H 296 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: H 318 GLN cc_start: 0.7990 (mp10) cc_final: 0.7399 (mp10) REVERT: J 251 MET cc_start: 0.5318 (mmt) cc_final: 0.4735 (mmt) outliers start: 85 outliers final: 47 residues processed: 501 average time/residue: 0.7406 time to fit residues: 414.4099 Evaluate side-chains 508 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 451 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 402 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 45 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 3 HIS C 35 GLN C 75 ASN C 105 GLN C 129 GLN D 58 ASN D 77 GLN E 44 GLN E 129 GLN E 218 ASN F 77 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 226 GLN H 246 ASN H 254 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118256 restraints weight = 32412.149| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.65 r_work: 0.3363 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22725 Z= 0.144 Angle : 0.545 11.587 31084 Z= 0.276 Chirality : 0.042 0.248 3467 Planarity : 0.004 0.049 3863 Dihedral : 13.173 94.567 3824 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.80 % Allowed : 23.97 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.03 (0.16), residues: 2651 helix: 2.15 (0.17), residues: 851 sheet: 1.42 (0.25), residues: 463 loop : -0.58 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 271 TYR 0.018 0.001 TYR G 321 PHE 0.010 0.001 PHE E 95 TRP 0.015 0.001 TRP G 266 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00336 (22725) covalent geometry : angle 0.54494 (31084) hydrogen bonds : bond 0.04118 ( 863) hydrogen bonds : angle 4.00881 ( 2443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 443 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7754 (mm) cc_final: 0.7375 (mt) REVERT: A 174 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6805 (ttp80) REVERT: B 51 LEU cc_start: 0.8697 (tp) cc_final: 0.8335 (tt) REVERT: B 183 TRP cc_start: 0.6825 (OUTLIER) cc_final: 0.6576 (t-100) REVERT: C 184 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: C 240 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8018 (ttpp) REVERT: D 24 ASP cc_start: 0.8286 (m-30) cc_final: 0.8084 (m-30) REVERT: D 121 ILE cc_start: 0.8601 (mp) cc_final: 0.8185 (mp) REVERT: D 127 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: D 238 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7636 (mttt) REVERT: E 13 VAL cc_start: 0.8645 (t) cc_final: 0.8396 (m) REVERT: E 120 ASP cc_start: 0.8147 (m-30) cc_final: 0.7918 (m-30) REVERT: E 295 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7780 (mmm160) REVERT: E 297 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8248 (mmmm) REVERT: F 17 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7951 (mt-10) REVERT: F 218 ASN cc_start: 0.8645 (m110) cc_final: 0.8393 (m110) REVERT: F 287 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8514 (mtp85) REVERT: F 289 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8391 (mtmm) REVERT: F 295 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.7675 (mtt-85) REVERT: G 75 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7981 (p0) REVERT: G 81 VAL cc_start: 0.8942 (m) cc_final: 0.8665 (p) REVERT: G 90 THR cc_start: 0.8093 (m) cc_final: 0.7854 (m) REVERT: G 118 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7807 (tm) REVERT: G 123 THR cc_start: 0.8272 (t) cc_final: 0.7961 (m) REVERT: G 197 GLU cc_start: 0.8238 (tp30) cc_final: 0.8016 (mm-30) REVERT: G 227 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7947 (mm-30) REVERT: G 228 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7442 (mt) REVERT: G 279 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7523 (mt-10) REVERT: G 297 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8012 (tmmm) REVERT: H 111 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7151 (t70) REVERT: H 156 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7935 (tm-30) REVERT: H 159 ARG cc_start: 0.8710 (ttt-90) cc_final: 0.8450 (ttt-90) REVERT: H 171 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7814 (mt-10) REVERT: H 197 GLU cc_start: 0.7897 (tp30) cc_final: 0.7624 (tp30) REVERT: H 238 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7753 (mtpp) REVERT: H 296 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: H 318 GLN cc_start: 0.7963 (mp10) cc_final: 0.7432 (mp10) REVERT: J 251 MET cc_start: 0.5313 (mmt) cc_final: 0.4680 (mmt) REVERT: J 404 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6344 (pmt-80) outliers start: 82 outliers final: 51 residues processed: 483 average time/residue: 0.7405 time to fit residues: 400.1402 Evaluate side-chains 509 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 445 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 260 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 236 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS B 142 GLN C 75 ASN C 105 GLN C 129 GLN D 58 ASN D 77 GLN E 44 GLN E 72 GLN E 129 GLN F 77 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 226 GLN H 246 ASN H 254 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117153 restraints weight = 32492.263| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.68 r_work: 0.3351 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22725 Z= 0.162 Angle : 0.554 10.623 31084 Z= 0.282 Chirality : 0.043 0.258 3467 Planarity : 0.004 0.046 3863 Dihedral : 13.187 94.879 3824 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.43 % Allowed : 24.39 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.98 (0.16), residues: 2651 helix: 2.10 (0.17), residues: 858 sheet: 1.33 (0.25), residues: 469 loop : -0.60 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 271 TYR 0.020 0.001 TYR G 321 PHE 0.012 0.001 PHE G 95 TRP 0.018 0.001 TRP G 266 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00383 (22725) covalent geometry : angle 0.55367 (31084) hydrogen bonds : bond 0.04314 ( 863) hydrogen bonds : angle 4.06900 ( 2443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 454 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7763 (mm) cc_final: 0.7386 (mt) REVERT: A 174 ARG cc_start: 0.7342 (ttp80) cc_final: 0.6899 (ttp80) REVERT: A 224 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: B 51 LEU cc_start: 0.8642 (tp) cc_final: 0.8289 (tt) REVERT: B 183 TRP cc_start: 0.6811 (OUTLIER) cc_final: 0.6550 (t-100) REVERT: C 184 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: C 240 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8009 (ttpp) REVERT: D 24 ASP cc_start: 0.8287 (m-30) cc_final: 0.8075 (m-30) REVERT: D 121 ILE cc_start: 0.8596 (mp) cc_final: 0.8167 (mp) REVERT: D 127 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: E 13 VAL cc_start: 0.8653 (t) cc_final: 0.8404 (m) REVERT: E 75 ASN cc_start: 0.8136 (m-40) cc_final: 0.7932 (m-40) REVERT: E 120 ASP cc_start: 0.8136 (m-30) cc_final: 0.7883 (m-30) REVERT: E 295 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7793 (mmm160) REVERT: E 297 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8259 (mmmm) REVERT: F 17 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7971 (mt-10) REVERT: F 218 ASN cc_start: 0.8665 (m110) cc_final: 0.8408 (m110) REVERT: F 227 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8116 (mm-30) REVERT: F 287 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8525 (mtp85) REVERT: F 289 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8397 (mtmm) REVERT: F 295 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7684 (mtt-85) REVERT: G 75 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7993 (p0) REVERT: G 81 VAL cc_start: 0.8928 (m) cc_final: 0.8660 (p) REVERT: G 90 THR cc_start: 0.8115 (m) cc_final: 0.7880 (m) REVERT: G 123 THR cc_start: 0.8272 (t) cc_final: 0.7963 (m) REVERT: G 197 GLU cc_start: 0.8268 (tp30) cc_final: 0.8016 (mm-30) REVERT: G 228 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7444 (mt) REVERT: G 279 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7524 (mt-10) REVERT: G 297 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8077 (tmmm) REVERT: H 156 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7944 (tm-30) REVERT: H 159 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8439 (ttt-90) REVERT: H 171 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7800 (mt-10) REVERT: H 197 GLU cc_start: 0.7895 (tp30) cc_final: 0.7601 (tp30) REVERT: H 198 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8463 (mmmm) REVERT: H 238 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7660 (mtpp) REVERT: H 296 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: H 318 GLN cc_start: 0.7986 (mp10) cc_final: 0.7402 (mp10) REVERT: J 251 MET cc_start: 0.5292 (mmt) cc_final: 0.4696 (mmt) REVERT: J 404 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6246 (pmt-80) outliers start: 74 outliers final: 48 residues processed: 495 average time/residue: 0.7701 time to fit residues: 424.5942 Evaluate side-chains 514 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 454 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 96 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 232 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS B 142 GLN C 75 ASN C 105 GLN C 129 GLN D 77 GLN E 44 GLN E 129 GLN F 77 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 226 GLN H 246 ASN H 254 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117530 restraints weight = 32285.560| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.65 r_work: 0.3356 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22725 Z= 0.165 Angle : 0.561 12.647 31084 Z= 0.284 Chirality : 0.043 0.272 3467 Planarity : 0.004 0.065 3863 Dihedral : 13.187 95.116 3824 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.29 % Allowed : 24.48 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.96 (0.16), residues: 2651 helix: 2.07 (0.17), residues: 858 sheet: 1.36 (0.25), residues: 463 loop : -0.60 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 271 TYR 0.020 0.001 TYR G 321 PHE 0.012 0.001 PHE G 95 TRP 0.021 0.001 TRP G 266 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00389 (22725) covalent geometry : angle 0.56057 (31084) hydrogen bonds : bond 0.04346 ( 863) hydrogen bonds : angle 4.06798 ( 2443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 453 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7765 (mm) cc_final: 0.7393 (mt) REVERT: A 174 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6893 (ttp80) REVERT: B 51 LEU cc_start: 0.8638 (tp) cc_final: 0.8284 (tt) REVERT: B 183 TRP cc_start: 0.6788 (OUTLIER) cc_final: 0.6523 (t-100) REVERT: C 184 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: C 240 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: D 24 ASP cc_start: 0.8279 (m-30) cc_final: 0.8068 (m-30) REVERT: D 121 ILE cc_start: 0.8603 (mp) cc_final: 0.8175 (mp) REVERT: D 127 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: E 13 VAL cc_start: 0.8632 (t) cc_final: 0.8384 (m) REVERT: E 75 ASN cc_start: 0.8154 (m-40) cc_final: 0.7942 (m-40) REVERT: E 120 ASP cc_start: 0.8133 (m-30) cc_final: 0.7878 (m-30) REVERT: E 295 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7786 (mmm160) REVERT: E 297 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8266 (mmmm) REVERT: F 17 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7969 (mt-10) REVERT: F 218 ASN cc_start: 0.8661 (m110) cc_final: 0.8403 (m110) REVERT: F 227 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8110 (mm-30) REVERT: F 287 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8506 (mtp85) REVERT: F 289 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8387 (mtmm) REVERT: F 295 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.7683 (mtt-85) REVERT: G 81 VAL cc_start: 0.8927 (m) cc_final: 0.8668 (p) REVERT: G 90 THR cc_start: 0.8110 (m) cc_final: 0.7887 (m) REVERT: G 123 THR cc_start: 0.8266 (t) cc_final: 0.7963 (m) REVERT: G 197 GLU cc_start: 0.8262 (tp30) cc_final: 0.7987 (mm-30) REVERT: G 227 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7980 (mm-30) REVERT: G 228 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7409 (mt) REVERT: G 279 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7486 (mt-10) REVERT: G 297 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8081 (tmmm) REVERT: H 156 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7932 (tm-30) REVERT: H 197 GLU cc_start: 0.7892 (tp30) cc_final: 0.7609 (tp30) REVERT: H 238 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7682 (mtpp) REVERT: H 296 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: H 318 GLN cc_start: 0.7985 (mp10) cc_final: 0.7408 (mp10) REVERT: J 251 MET cc_start: 0.5323 (mmt) cc_final: 0.4775 (mmt) REVERT: J 404 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6203 (pmt-80) outliers start: 71 outliers final: 53 residues processed: 490 average time/residue: 0.7586 time to fit residues: 414.3896 Evaluate side-chains 516 residues out of total 2158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 453 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 TRP Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 255 LYS Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain J residue 404 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 146 optimal weight: 1.9990 chunk 204 optimal weight: 0.0070 chunk 71 optimal weight: 0.9980 chunk 252 optimal weight: 40.0000 chunk 157 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS B 142 GLN C 75 ASN C 105 GLN C 129 GLN D 77 GLN E 44 GLN E 129 GLN F 77 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 226 GLN H 246 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118468 restraints weight = 32419.313| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.64 r_work: 0.3368 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22725 Z= 0.128 Angle : 0.543 11.355 31084 Z= 0.274 Chirality : 0.042 0.272 3467 Planarity : 0.004 0.041 3863 Dihedral : 13.152 95.467 3824 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.06 % Allowed : 24.76 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.06 (0.16), residues: 2651 helix: 2.16 (0.18), residues: 857 sheet: 1.41 (0.25), residues: 467 loop : -0.56 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.017 0.001 TYR G 321 PHE 0.010 0.001 PHE G 300 TRP 0.016 0.001 TRP G 266 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00296 (22725) covalent geometry : angle 0.54348 (31084) hydrogen bonds : bond 0.03949 ( 863) hydrogen bonds : angle 3.97034 ( 2443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11038.56 seconds wall clock time: 187 minutes 46.07 seconds (11266.07 seconds total)