Starting phenix.real_space_refine on Tue Aug 26 13:42:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ee4_28045/08_2025/8ee4_28045.map" } resolution = 2.6 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= -0.001 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 94 5.16 5 C 11917 2.51 5 N 3328 2.21 5 O 3530 1.98 5 H 18599 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37480 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6046 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5987 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 6407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6407 Classifications: {'peptide': 403} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 6260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6260 Classifications: {'peptide': 393} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 6335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6335 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 381} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 6321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6321 Classifications: {'peptide': 396} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.51, per 1000 atoms: 0.17 Number of scatterers: 37480 At special positions: 0 Unit cell: (134.4, 115.36, 133.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 12 15.00 O 3530 8.00 N 3328 7.00 C 11917 6.00 H 18599 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 902.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 24 sheets defined 46.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.648A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.660A pdb=" N SER A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.572A pdb=" N LEU A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.670A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.516A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 removed outlier: 3.803A pdb=" N PHE A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 251 removed outlier: 4.353A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.615A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.565A pdb=" N GLN A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.549A pdb=" N SER A 358 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.649A pdb=" N LEU B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.648A pdb=" N SER B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 59 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.580A pdb=" N LEU B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 66 " --> pdb=" O LYS B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.838A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.535A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 192 through 217 removed outlier: 3.719A pdb=" N PHE B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 251 removed outlier: 3.858A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.610A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.579A pdb=" N GLN B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.519A pdb=" N SER B 358 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 34 through 47 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.732A pdb=" N ILE C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 6.694A pdb=" N ALA C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 118 through 137 removed outlier: 3.615A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.525A pdb=" N TYR C 183 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.791A pdb=" N TRP C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 225 through 251 removed outlier: 3.578A pdb=" N ILE C 235 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLN C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 302 removed outlier: 3.786A pdb=" N ARG C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.640A pdb=" N THR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 359 through 360 No H-bonds generated for 'chain 'C' and resid 359 through 360' Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 389 through 397 removed outlier: 3.505A pdb=" N VAL C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.563A pdb=" N ALA C 410 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 53 Proline residue: D 49 - end of helix removed outlier: 3.637A pdb=" N GLY D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 3.768A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL D 60 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 118 through 137 removed outlier: 3.983A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 193 through 217 removed outlier: 3.574A pdb=" N SER D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 247 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 329 through 332 removed outlier: 3.597A pdb=" N GLN D 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 332' Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.042A pdb=" N LEU D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 360 No H-bonds generated for 'chain 'D' and resid 359 through 360' Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 389 through 397 Processing helix chain 'E' and resid 35 through 53 removed outlier: 3.654A pdb=" N PHE E 48 " --> pdb=" O ARG E 44 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.701A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.613A pdb=" N ALA E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 118 through 137 removed outlier: 3.697A pdb=" N ALA E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 removed outlier: 3.553A pdb=" N TYR E 183 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 184 " --> pdb=" O SER E 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 184' Processing helix chain 'E' and resid 192 through 217 removed outlier: 4.043A pdb=" N PHE E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU E 215 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 217 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 247 removed outlier: 4.169A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE E 235 " --> pdb=" O MET E 231 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 302 removed outlier: 3.805A pdb=" N ARG E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 306 Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.718A pdb=" N THR E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 359 through 360 No H-bonds generated for 'chain 'E' and resid 359 through 360' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 389 through 398 removed outlier: 3.543A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.663A pdb=" N ALA F 66 " --> pdb=" O LYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 118 through 136 removed outlier: 3.661A pdb=" N LEU F 124 " --> pdb=" O MET F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 184 removed outlier: 3.850A pdb=" N GLY F 182 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 183 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 217 removed outlier: 3.825A pdb=" N PHE F 196 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 removed outlier: 5.174A pdb=" N LEU F 222 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU F 224 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 247 removed outlier: 3.731A pdb=" N GLN F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 281 through 302 removed outlier: 3.779A pdb=" N ASN F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 329 through 332 removed outlier: 3.573A pdb=" N GLN F 332 " --> pdb=" O ALA F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 332' Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 353 through 358 removed outlier: 3.989A pdb=" N LEU F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 360 No H-bonds generated for 'chain 'F' and resid 359 through 360' Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 389 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.925A pdb=" N LYS A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 6.485A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR A 26 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR A 351 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 28 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 5.609A pdb=" N ASP A 254 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 268 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.850A pdb=" N THR B 94 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 6 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 92 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU B 8 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS B 90 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 152 removed outlier: 6.490A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR B 26 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR B 351 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 28 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.339A pdb=" N ILE C 3 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU C 96 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 148 through 152 removed outlier: 6.322A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG C 366 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE C 27 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU C 368 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 29 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN C 370 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 74 removed outlier: 4.400A pdb=" N ARG C 73 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 253 through 258 removed outlier: 5.434A pdb=" N ASP C 254 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER C 268 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 258 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 264 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.633A pdb=" N ILE D 91 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 152 removed outlier: 6.462A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ARG D 366 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE D 27 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU D 368 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 73 through 77 removed outlier: 4.383A pdb=" N ARG D 73 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 86 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG D 77 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN D 82 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 96 through 97 Processing sheet with id=AB8, first strand: chain 'D' and resid 253 through 258 removed outlier: 5.558A pdb=" N ASP D 254 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER D 268 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 16 through 20 removed outlier: 5.570A pdb=" N ILE E 3 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU E 96 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 97 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LYS E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 148 through 152 removed outlier: 6.302A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ARG E 366 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE E 27 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU E 368 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 29 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLN E 370 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 253 through 258 removed outlier: 5.490A pdb=" N ASP E 254 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER E 268 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 258 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 264 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 16 through 19 removed outlier: 7.002A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 147 through 152 removed outlier: 6.528A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC6, first strand: chain 'F' and resid 253 through 258 removed outlier: 5.605A pdb=" N ASP F 254 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER F 268 " --> pdb=" O ASP F 254 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18576 1.03 - 1.23: 30 1.23 - 1.42: 8025 1.42 - 1.61: 11081 1.61 - 1.81: 164 Bond restraints: 37876 Sorted by residual: bond pdb=" CA PRO A 114 " pdb=" C PRO A 114 " ideal model delta sigma weight residual 1.514 1.523 -0.008 5.50e-03 3.31e+04 2.33e+00 bond pdb=" C PRO D 114 " pdb=" O PRO D 114 " ideal model delta sigma weight residual 1.246 1.236 0.010 8.50e-03 1.38e+04 1.26e+00 bond pdb=" N PRO D 114 " pdb=" CA PRO D 114 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.14e+00 bond pdb=" CB VAL A 135 " pdb=" CG1 VAL A 135 " ideal model delta sigma weight residual 1.521 1.552 -0.031 3.30e-02 9.18e+02 9.01e-01 bond pdb=" CG LEU B 215 " pdb=" CD2 LEU B 215 " ideal model delta sigma weight residual 1.521 1.552 -0.031 3.30e-02 9.18e+02 8.88e-01 ... (remaining 37871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 68307 5.41 - 10.83: 44 10.83 - 16.24: 2 16.24 - 21.65: 0 21.65 - 27.07: 33 Bond angle restraints: 68386 Sorted by residual: angle pdb=" CG2 VAL A 135 " pdb=" CB VAL A 135 " pdb=" HB VAL A 135 " ideal model delta sigma weight residual 108.00 80.93 27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" CG2 VAL B 135 " pdb=" CB VAL B 135 " pdb=" HB VAL B 135 " ideal model delta sigma weight residual 108.00 81.19 26.81 3.00e+00 1.11e-01 7.99e+01 angle pdb=" CG1 VAL A 135 " pdb=" CB VAL A 135 " pdb=" HB VAL A 135 " ideal model delta sigma weight residual 108.00 81.51 26.49 3.00e+00 1.11e-01 7.80e+01 angle pdb=" CG1 VAL B 135 " pdb=" CB VAL B 135 " pdb=" HB VAL B 135 " ideal model delta sigma weight residual 108.00 81.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CG1 VAL A 226 " pdb=" CB VAL A 226 " pdb=" HB VAL A 226 " ideal model delta sigma weight residual 108.00 81.76 26.24 3.00e+00 1.11e-01 7.65e+01 ... (remaining 68381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16029 17.93 - 35.87: 1277 35.87 - 53.80: 365 53.80 - 71.74: 87 71.74 - 89.67: 27 Dihedral angle restraints: 17785 sinusoidal: 9862 harmonic: 7923 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU D 305 " pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU E 305 " pdb=" C LEU E 305 " pdb=" N GLN E 306 " pdb=" CA GLN E 306 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 2880 0.344 - 0.687: 0 0.687 - 1.031: 0 1.031 - 1.375: 2 1.375 - 1.719: 9 Chirality restraints: 2891 Sorted by residual: chirality pdb=" CG LEU D 65 " pdb=" CB LEU D 65 " pdb=" CD1 LEU D 65 " pdb=" CD2 LEU D 65 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.38e+01 chirality pdb=" CG LEU A 157 " pdb=" CB LEU A 157 " pdb=" CD1 LEU A 157 " pdb=" CD2 LEU A 157 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.25e+01 chirality pdb=" CG LEU C 203 " pdb=" CB LEU C 203 " pdb=" CD1 LEU C 203 " pdb=" CD2 LEU C 203 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.14e+01 ... (remaining 2888 not shown) Planarity restraints: 5571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 113 " 0.016 2.00e-02 2.50e+03 1.88e-02 5.28e+00 pdb=" CD GLN D 113 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN D 113 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN D 113 " 0.008 2.00e-02 2.50e+03 pdb="HE21 GLN D 113 " -0.004 2.00e-02 2.50e+03 pdb="HE22 GLN D 113 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 269 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 270 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 269 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 270 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.029 5.00e-02 4.00e+02 ... (remaining 5568 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1310 2.18 - 2.78: 72123 2.78 - 3.39: 98555 3.39 - 3.99: 131644 3.99 - 4.60: 208866 Nonbonded interactions: 512498 Sorted by model distance: nonbonded pdb=" OE1 GLU A 224 " pdb="HE21 GLN E 78 " model vdw 1.569 2.450 nonbonded pdb=" O GLN D 16 " pdb=" H GLY D 376 " model vdw 1.585 2.450 nonbonded pdb=" O CYS D 244 " pdb="HE22 GLN D 248 " model vdw 1.614 2.450 nonbonded pdb=" O ALA D 309 " pdb=" HG1 THR D 313 " model vdw 1.615 2.450 nonbonded pdb=" OE1 GLU B 164 " pdb=" H GLU B 164 " model vdw 1.616 2.450 ... (remaining 512493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or resid 3 thr \ ough 12 or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me SG or name H or name HA or name HB2 or name HB3)) or resid 14 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) \ or resid 38 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12)) or resid 137 through 159 or \ (resid 160 and (name CA or name C or name O or name CB )) or resid 171 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 195 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) o \ r resid 196 through 219 or (resid 225 and (name N or name CA or name C or name O \ or name HA2 or name HA3)) or resid 226 through 238 or (resid 239 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2 or name H or name HA )) or resid 240 through 369 or (resid 370 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) \ or resid 371 through 382)) selection = (chain 'B' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or resid 3 thr \ ough 12 or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me SG or name H or name HA or name HB2 or name HB3)) or resid 14 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) \ or resid 38 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12)) or resid 137 through 159 or \ (resid 160 and (name CA or name C or name O or name CB )) or resid 171 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE or name NZ )) or (resid 195 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) o \ r resid 196 through 219 or (resid 225 and (name N or name CA or name C or name O \ or name HA2 or name HA3)) or resid 226 through 238 or (resid 239 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2 or name H or name HA )) or resid 240 through 369 or (resid 370 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) \ or resid 371 through 382)) selection = (chain 'C' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 14 through 36 or (resid 37 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 o \ r name HG22 or name HG23)) or resid 38 through 135 or (resid 136 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) o \ r resid 137 through 159 or (resid 160 and (name CA or name C or name O or name C \ B )) or (resid 171 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12 or name HH21 or name HH22)) or resid 172 through 193 or (re \ sid 194 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 195 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2 or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 1 \ 96 through 219 or (resid 225 and (name N or name CA or name C or name O or name \ HA2 or name HA3)) or resid 226 through 238 or (resid 239 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 or \ name H or name HA )) or resid 240 through 369 or (resid 370 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid \ 371 through 382)) selection = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 3 through 135 or (resid 136 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH12)) or resid 137 through 170 or (res \ id 171 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or n \ ame HH12 or name HH21 or name HH22)) or resid 172 through 193 or (resid 194 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE or name NZ )) or (resid 195 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or nam \ e HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 196 through 2 \ 19 or resid 225 through 382)) selection = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or resid 3 thr \ ough 12 or (resid 13 and (name N or name CA or name C or name O or name CB or na \ me SG or name H or name HA or name HB2 or name HB3)) or resid 14 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) \ or resid 38 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12)) or resid 137 through 159 or \ (resid 160 and (name CA or name C or name O or name CB )) or (resid 171 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or nam \ e HH21 or name HH22)) or resid 172 through 219 or (resid 225 and (name N or name \ CA or name C or name O or name HA2 or name HA3)) or resid 226 through 238 or (r \ esid 239 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name NE2 or name H or name HA )) or resid 240 through 369 or \ (resid 370 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3)) or resid 371 through 382)) selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or \ resid 3 through 12 or (resid 13 and (name N or name CA or name C or name O or na \ me CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 14 thro \ ugh 36 or (resid 37 and (name N or name CA or name C or name O or name CB or nam \ e OG1 or name CG2 or name H or name HA or name HB or name HG21 or name HG22 or n \ ame HG23)) or resid 38 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 140 through 159 or (resid 170 and (name CA or name C or name O or name CB )) o \ r (resid 171 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH1 \ 1 or name HH12 or name HH21 or name HH22)) or resid 172 through 193 or (resid 19 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ )) or (resid 195 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 196 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD2 or name HE1)) or resid 211 through 219 or (resi \ d 225 and (name N or name CA or name C or name O or name HA2 or name HA3)) or re \ sid 226 through 238 or (resid 239 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) or \ resid 240 through 252 or (resid 253 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 254 throug \ h 260 or (resid 261 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or nam \ e HB2 or name HB3 or name HD2 or name HE1)) or resid 262 through 303 or (resid 3 \ 04 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 \ or name HD2 or name HE1)) or resid 305 through 326 or (resid 327 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or na \ me CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or n \ ame HE1)) or resid 328 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 353 through 369 or (resid 370 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3)) or resid 371 through 382)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 32.340 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.002 0.031 19277 Z= 0.116 Angle : 0.629 11.147 26132 Z= 0.329 Chirality : 0.106 1.719 2891 Planarity : 0.004 0.056 3346 Dihedral : 15.547 89.382 7306 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.75 (0.17), residues: 2310 helix: 0.17 (0.18), residues: 825 sheet: -0.41 (0.23), residues: 449 loop : -0.99 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.016 0.001 TYR E 200 PHE 0.017 0.001 PHE B 11 TRP 0.017 0.001 TRP F 199 HIS 0.013 0.001 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00247 (19277) covalent geometry : angle 0.62902 (26132) hydrogen bonds : bond 0.16294 ( 829) hydrogen bonds : angle 6.38139 ( 2238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8646 (p0) cc_final: 0.8368 (p0) REVERT: A 248 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 85 MET cc_start: 0.8719 (ttm) cc_final: 0.8222 (ttm) REVERT: B 134 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7998 (mtp180) REVERT: D 83 MET cc_start: 0.2793 (mmt) cc_final: 0.2524 (mmt) REVERT: D 106 MET cc_start: 0.7224 (ttp) cc_final: 0.6767 (mtm) REVERT: D 377 LYS cc_start: 0.5858 (ttmm) cc_final: 0.5569 (tppt) REVERT: F 5 LYS cc_start: 0.8245 (tttp) cc_final: 0.7612 (ttpt) REVERT: F 18 ASP cc_start: 0.5067 (t70) cc_final: 0.4863 (t70) REVERT: F 391 ASN cc_start: 0.5564 (m110) cc_final: 0.4916 (p0) outliers start: 0 outliers final: 2 residues processed: 298 average time/residue: 1.2772 time to fit residues: 423.2129 Evaluate side-chains 227 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain D residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 GLN C 370 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN E 370 GLN F 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.195822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142364 restraints weight = 49903.264| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.30 r_work: 0.3245 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19277 Z= 0.177 Angle : 0.664 11.379 26132 Z= 0.349 Chirality : 0.106 1.704 2891 Planarity : 0.005 0.055 3346 Dihedral : 9.214 87.685 2664 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.83 % Allowed : 7.46 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.66 (0.17), residues: 2310 helix: 0.46 (0.18), residues: 807 sheet: -0.55 (0.23), residues: 448 loop : -1.01 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.016 0.002 TYR A 272 PHE 0.017 0.002 PHE E 296 TRP 0.016 0.002 TRP D 199 HIS 0.006 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00409 (19277) covalent geometry : angle 0.66430 (26132) hydrogen bonds : bond 0.06692 ( 829) hydrogen bonds : angle 5.28908 ( 2238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8669 (p0) cc_final: 0.8387 (p0) REVERT: B 85 MET cc_start: 0.8839 (ttm) cc_final: 0.8344 (ttm) REVERT: D 16 GLN cc_start: 0.6756 (tm-30) cc_final: 0.6083 (tp40) REVERT: D 70 GLU cc_start: 0.5166 (mp0) cc_final: 0.4952 (mp0) REVERT: D 145 GLU cc_start: 0.6215 (mt-10) cc_final: 0.6015 (mt-10) REVERT: D 377 LYS cc_start: 0.5393 (ttmm) cc_final: 0.4559 (tppt) REVERT: F 391 ASN cc_start: 0.5198 (m110) cc_final: 0.4042 (p0) outliers start: 17 outliers final: 10 residues processed: 238 average time/residue: 1.1405 time to fit residues: 305.3069 Evaluate side-chains 229 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 244 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 225 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 395 GLN D 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.195789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140893 restraints weight = 49716.921| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.43 r_work: 0.3215 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19277 Z= 0.155 Angle : 0.641 11.199 26132 Z= 0.334 Chirality : 0.105 1.704 2891 Planarity : 0.005 0.055 3346 Dihedral : 8.730 87.622 2662 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.88 % Allowed : 8.93 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.62 (0.17), residues: 2310 helix: 0.58 (0.18), residues: 807 sheet: -0.57 (0.23), residues: 441 loop : -1.05 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 156 TYR 0.016 0.001 TYR A 272 PHE 0.016 0.002 PHE E 196 TRP 0.016 0.002 TRP D 199 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00358 (19277) covalent geometry : angle 0.64140 (26132) hydrogen bonds : bond 0.06116 ( 829) hydrogen bonds : angle 5.02412 ( 2238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8656 (p0) cc_final: 0.8366 (p0) REVERT: B 85 MET cc_start: 0.8844 (ttm) cc_final: 0.8334 (ttm) REVERT: C 195 GLN cc_start: 0.7984 (pt0) cc_final: 0.7682 (pt0) REVERT: D 1 MET cc_start: 0.7692 (tpt) cc_final: 0.7197 (tpt) REVERT: D 16 GLN cc_start: 0.6891 (tm-30) cc_final: 0.5972 (tm-30) REVERT: D 134 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.4722 (ttp-110) REVERT: D 377 LYS cc_start: 0.5426 (ttmm) cc_final: 0.4602 (tppt) REVERT: E 77 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.7205 (mtm-85) REVERT: E 232 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6374 (tttt) REVERT: F 7 SER cc_start: 0.7407 (t) cc_final: 0.7198 (p) REVERT: F 389 PRO cc_start: 0.5785 (Cg_endo) cc_final: 0.5512 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5213 (m110) cc_final: 0.3951 (p0) outliers start: 18 outliers final: 8 residues processed: 240 average time/residue: 1.2291 time to fit residues: 330.7641 Evaluate side-chains 238 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 18 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 189 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 ASN C 195 GLN C 395 GLN D 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.195360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139094 restraints weight = 49724.057| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.41 r_work: 0.3240 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19277 Z= 0.163 Angle : 0.643 11.127 26132 Z= 0.336 Chirality : 0.105 1.707 2891 Planarity : 0.005 0.055 3346 Dihedral : 8.527 88.318 2662 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.08 % Allowed : 10.55 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.60 (0.17), residues: 2310 helix: 0.59 (0.18), residues: 812 sheet: -0.59 (0.23), residues: 441 loop : -1.03 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 339 TYR 0.013 0.001 TYR A 272 PHE 0.018 0.002 PHE E 296 TRP 0.016 0.002 TRP D 199 HIS 0.006 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00381 (19277) covalent geometry : angle 0.64331 (26132) hydrogen bonds : bond 0.06052 ( 829) hydrogen bonds : angle 4.93984 ( 2238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8829 (ttm) cc_final: 0.8305 (ttm) REVERT: B 134 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7982 (mtp180) REVERT: C 195 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: D 16 GLN cc_start: 0.6869 (tm-30) cc_final: 0.5974 (tm-30) REVERT: D 134 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4698 (ttp-110) REVERT: D 377 LYS cc_start: 0.5420 (ttmm) cc_final: 0.4606 (tppt) REVERT: E 77 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7168 (mtm-85) REVERT: E 362 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7525 (ptm-80) REVERT: F 389 PRO cc_start: 0.5750 (Cg_endo) cc_final: 0.5459 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5274 (m110) cc_final: 0.3975 (p0) outliers start: 22 outliers final: 16 residues processed: 244 average time/residue: 1.2483 time to fit residues: 341.0402 Evaluate side-chains 247 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 229 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 125 optimal weight: 0.0000 chunk 98 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 240 GLN C 395 GLN D 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.194982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139233 restraints weight = 49592.111| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.34 r_work: 0.3229 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19277 Z= 0.174 Angle : 0.651 11.196 26132 Z= 0.340 Chirality : 0.106 1.705 2891 Planarity : 0.005 0.055 3346 Dihedral : 8.545 86.255 2662 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.03 % Allowed : 11.34 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.63 (0.17), residues: 2310 helix: 0.56 (0.18), residues: 813 sheet: -0.61 (0.23), residues: 441 loop : -1.05 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 339 TYR 0.012 0.002 TYR B 193 PHE 0.018 0.002 PHE A 296 TRP 0.016 0.002 TRP F 199 HIS 0.006 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00410 (19277) covalent geometry : angle 0.65108 (26132) hydrogen bonds : bond 0.06191 ( 829) hydrogen bonds : angle 4.92246 ( 2238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.8819 (ttm) cc_final: 0.8293 (ttm) REVERT: B 134 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8042 (mtp180) REVERT: D 1 MET cc_start: 0.7652 (tpt) cc_final: 0.7256 (tpt) REVERT: D 16 GLN cc_start: 0.6864 (tm-30) cc_final: 0.5977 (tm-30) REVERT: D 134 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.4701 (ttp-110) REVERT: D 377 LYS cc_start: 0.5418 (ttmm) cc_final: 0.4609 (tppt) REVERT: E 77 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7166 (mtm-85) REVERT: E 362 ARG cc_start: 0.7764 (ptm-80) cc_final: 0.7514 (ptm-80) REVERT: F 389 PRO cc_start: 0.5912 (Cg_endo) cc_final: 0.5659 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5334 (m110) cc_final: 0.4024 (p0) outliers start: 21 outliers final: 18 residues processed: 241 average time/residue: 1.2889 time to fit residues: 347.7088 Evaluate side-chains 245 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 39 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 395 GLN D 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.206287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142964 restraints weight = 51635.341| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.82 r_work: 0.3489 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19277 Z= 0.140 Angle : 0.617 11.120 26132 Z= 0.321 Chirality : 0.105 1.709 2891 Planarity : 0.005 0.055 3346 Dihedral : 8.395 87.616 2662 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.13 % Allowed : 11.98 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.48 (0.17), residues: 2310 helix: 0.73 (0.18), residues: 814 sheet: -0.58 (0.23), residues: 441 loop : -0.98 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 362 TYR 0.011 0.001 TYR C 207 PHE 0.021 0.002 PHE F 50 TRP 0.016 0.001 TRP F 199 HIS 0.005 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00322 (19277) covalent geometry : angle 0.61734 (26132) hydrogen bonds : bond 0.05518 ( 829) hydrogen bonds : angle 4.82459 ( 2238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8623 (p0) cc_final: 0.8344 (p0) REVERT: B 85 MET cc_start: 0.8798 (ttm) cc_final: 0.8287 (ttm) REVERT: B 134 ARG cc_start: 0.8284 (mtp180) cc_final: 0.8038 (mtp180) REVERT: D 1 MET cc_start: 0.7636 (tpt) cc_final: 0.7272 (tpt) REVERT: D 16 GLN cc_start: 0.6814 (tm-30) cc_final: 0.5841 (tm-30) REVERT: D 134 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.4623 (ttp-110) REVERT: D 377 LYS cc_start: 0.5352 (ttmm) cc_final: 0.4535 (tppt) REVERT: E 77 ARG cc_start: 0.7439 (mtp-110) cc_final: 0.7179 (mtm-85) REVERT: F 389 PRO cc_start: 0.5798 (Cg_endo) cc_final: 0.5518 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5336 (m110) cc_final: 0.4001 (p0) outliers start: 23 outliers final: 18 residues processed: 242 average time/residue: 1.2685 time to fit residues: 343.6728 Evaluate side-chains 247 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 127 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 195 GLN C 395 GLN D 264 GLN E 395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.205433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141567 restraints weight = 51650.724| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.55 r_work: 0.3494 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19277 Z= 0.167 Angle : 0.644 11.207 26132 Z= 0.336 Chirality : 0.105 1.704 2891 Planarity : 0.005 0.056 3346 Dihedral : 8.428 88.122 2662 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.23 % Allowed : 12.62 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.56 (0.17), residues: 2310 helix: 0.65 (0.18), residues: 814 sheet: -0.60 (0.23), residues: 441 loop : -1.02 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.012 0.001 TYR B 193 PHE 0.019 0.002 PHE A 296 TRP 0.016 0.002 TRP D 199 HIS 0.006 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00395 (19277) covalent geometry : angle 0.64373 (26132) hydrogen bonds : bond 0.06020 ( 829) hydrogen bonds : angle 4.83423 ( 2238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8615 (p0) cc_final: 0.8356 (p0) REVERT: B 85 MET cc_start: 0.8779 (ttm) cc_final: 0.8266 (ttm) REVERT: B 134 ARG cc_start: 0.8273 (mtp180) cc_final: 0.8020 (mtp180) REVERT: D 1 MET cc_start: 0.7722 (tpt) cc_final: 0.7360 (tpt) REVERT: D 16 GLN cc_start: 0.6814 (tm-30) cc_final: 0.5870 (tm-30) REVERT: D 134 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.4654 (ttp-110) REVERT: D 377 LYS cc_start: 0.5342 (ttmm) cc_final: 0.4553 (tppt) REVERT: E 362 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7590 (ptm-80) REVERT: F 389 PRO cc_start: 0.5846 (Cg_endo) cc_final: 0.5583 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5386 (m110) cc_final: 0.4086 (p0) outliers start: 25 outliers final: 18 residues processed: 246 average time/residue: 1.2485 time to fit residues: 344.8675 Evaluate side-chains 244 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 195 GLN C 395 GLN D 264 GLN D 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.205110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141116 restraints weight = 51373.238| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.54 r_work: 0.3489 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19277 Z= 0.172 Angle : 0.649 11.112 26132 Z= 0.339 Chirality : 0.105 1.709 2891 Planarity : 0.005 0.057 3346 Dihedral : 8.441 89.884 2662 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.28 % Allowed : 13.16 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.65 (0.17), residues: 2310 helix: 0.56 (0.18), residues: 821 sheet: -0.61 (0.23), residues: 442 loop : -1.09 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.012 0.002 TYR B 193 PHE 0.018 0.002 PHE A 296 TRP 0.023 0.002 TRP F 158 HIS 0.007 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00405 (19277) covalent geometry : angle 0.64887 (26132) hydrogen bonds : bond 0.06092 ( 829) hydrogen bonds : angle 4.84501 ( 2238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.8786 (ttm) cc_final: 0.8280 (ttm) REVERT: B 134 ARG cc_start: 0.8260 (mtp180) cc_final: 0.8015 (mtp180) REVERT: D 1 MET cc_start: 0.7682 (tpt) cc_final: 0.7355 (tpt) REVERT: D 16 GLN cc_start: 0.6777 (tm-30) cc_final: 0.5888 (tm-30) REVERT: D 134 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.4647 (ttp-110) REVERT: D 195 GLN cc_start: 0.6757 (mm-40) cc_final: 0.6478 (mp10) REVERT: D 377 LYS cc_start: 0.5338 (ttmm) cc_final: 0.4551 (tppt) REVERT: E 362 ARG cc_start: 0.7871 (ptm-80) cc_final: 0.7597 (ptm-80) REVERT: F 389 PRO cc_start: 0.5901 (Cg_endo) cc_final: 0.5634 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5445 (m110) cc_final: 0.4102 (p0) outliers start: 26 outliers final: 21 residues processed: 242 average time/residue: 1.2437 time to fit residues: 337.0796 Evaluate side-chains 246 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 181 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN B 240 GLN C 195 GLN C 395 GLN D 264 GLN E 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.203207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141127 restraints weight = 51581.673| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.75 r_work: 0.3429 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19277 Z= 0.239 Angle : 0.721 11.760 26132 Z= 0.379 Chirality : 0.106 1.735 2891 Planarity : 0.006 0.058 3346 Dihedral : 8.453 81.409 2662 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.33 % Allowed : 13.25 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.89 (0.17), residues: 2310 helix: 0.26 (0.18), residues: 826 sheet: -0.66 (0.23), residues: 442 loop : -1.19 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.016 0.002 TYR B 193 PHE 0.021 0.002 PHE A 296 TRP 0.022 0.002 TRP F 158 HIS 0.008 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00573 (19277) covalent geometry : angle 0.72072 (26132) hydrogen bonds : bond 0.07200 ( 829) hydrogen bonds : angle 4.97317 ( 2238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.8788 (ttm) cc_final: 0.8287 (ttm) REVERT: B 134 ARG cc_start: 0.8326 (mtp180) cc_final: 0.8114 (mtp180) REVERT: C 159 TYR cc_start: 0.5191 (t80) cc_final: 0.4755 (t80) REVERT: D 16 GLN cc_start: 0.6744 (tm-30) cc_final: 0.5927 (tm-30) REVERT: D 134 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.4638 (ttp-110) REVERT: D 377 LYS cc_start: 0.5374 (ttmm) cc_final: 0.4570 (tppt) REVERT: E 77 ARG cc_start: 0.7492 (mtp-110) cc_final: 0.7244 (mtm-85) REVERT: E 232 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6344 (tttt) REVERT: E 362 ARG cc_start: 0.7926 (ptm-80) cc_final: 0.7624 (ptm-80) REVERT: F 16 GLN cc_start: 0.6529 (pp30) cc_final: 0.6048 (pp30) REVERT: F 389 PRO cc_start: 0.5914 (Cg_endo) cc_final: 0.5636 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5445 (m110) cc_final: 0.4065 (p0) outliers start: 27 outliers final: 18 residues processed: 248 average time/residue: 1.3353 time to fit residues: 370.3943 Evaluate side-chains 247 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 271 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 195 GLN D 264 GLN D 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.197238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141887 restraints weight = 49706.712| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.42 r_work: 0.3254 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19277 Z= 0.112 Angle : 0.594 11.094 26132 Z= 0.307 Chirality : 0.104 1.731 2891 Planarity : 0.004 0.057 3346 Dihedral : 7.881 70.052 2660 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.13 % Allowed : 13.75 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.48 (0.17), residues: 2310 helix: 0.77 (0.18), residues: 818 sheet: -0.59 (0.23), residues: 440 loop : -1.01 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 362 TYR 0.009 0.001 TYR B 163 PHE 0.013 0.001 PHE E 196 TRP 0.016 0.001 TRP D 199 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00244 (19277) covalent geometry : angle 0.59394 (26132) hydrogen bonds : bond 0.04789 ( 829) hydrogen bonds : angle 4.74809 ( 2238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 37 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.8594 (p0) cc_final: 0.8269 (p0) REVERT: B 85 MET cc_start: 0.8772 (ttm) cc_final: 0.8261 (ttm) REVERT: D 16 GLN cc_start: 0.6753 (tm-30) cc_final: 0.5855 (tm-30) REVERT: D 336 GLN cc_start: 0.7957 (pt0) cc_final: 0.7732 (pt0) REVERT: D 377 LYS cc_start: 0.5272 (ttmm) cc_final: 0.4492 (tppt) REVERT: E 77 ARG cc_start: 0.7418 (mtp-110) cc_final: 0.7172 (mtm-85) REVERT: E 362 ARG cc_start: 0.7804 (ptm-80) cc_final: 0.7560 (ptm-80) REVERT: F 389 PRO cc_start: 0.5869 (Cg_endo) cc_final: 0.5589 (Cg_endo) REVERT: F 391 ASN cc_start: 0.5359 (m110) cc_final: 0.4019 (p0) outliers start: 23 outliers final: 15 residues processed: 247 average time/residue: 1.3413 time to fit residues: 373.3211 Evaluate side-chains 248 residues out of total 2043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 244 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 244 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 134 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN D 264 GLN D 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144204 restraints weight = 49819.459| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.30 r_work: 0.3278 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19277 Z= 0.113 Angle : 0.587 11.113 26132 Z= 0.302 Chirality : 0.104 1.707 2891 Planarity : 0.004 0.052 3346 Dihedral : 7.576 73.375 2660 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.79 % Allowed : 14.09 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.25 (0.17), residues: 2310 helix: 1.08 (0.18), residues: 809 sheet: -0.61 (0.22), residues: 458 loop : -0.90 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 230 TYR 0.010 0.001 TYR C 207 PHE 0.021 0.001 PHE F 50 TRP 0.015 0.001 TRP D 199 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00255 (19277) covalent geometry : angle 0.58700 (26132) hydrogen bonds : bond 0.04660 ( 829) hydrogen bonds : angle 4.62758 ( 2238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12832.80 seconds wall clock time: 217 minutes 5.89 seconds (13025.89 seconds total)