Starting phenix.real_space_refine on Sat Jul 4 14:34:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs4_29413/07_2026/8fs4_29413.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 55 5.49 5 Mg 4 5.21 5 S 112 5.16 5 C 13352 2.51 5 N 3657 2.21 5 O 4111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21291 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3466 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 16, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2482 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 1 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2184 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 10 Chain: "G" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2265 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 4, 'TRANS': 281} Chain breaks: 3 Chain: "H" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1930 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 9 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 2 Chain: "J" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 151 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.16 Number of scatterers: 21291 At special positions: 0 Unit cell: (117.576, 136.62, 138.276, 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 112 16.00 P 55 15.00 Mg 4 11.99 O 4111 8.00 N 3657 7.00 C 13352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 994.8 milliseconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 16 sheets defined 52.9% alpha, 14.4% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.621A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.914A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.613A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 4.170A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.614A pdb=" N ASP A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 498 Proline residue: A 489 - end of helix removed outlier: 3.800A pdb=" N SER A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.520A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.566A pdb=" N VAL B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 93 through 99 removed outlier: 3.517A pdb=" N ALA B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.854A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.807A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.522A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.728A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.531A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.570A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.665A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.577A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.861A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.718A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.033A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.529A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.065A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.014A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.938A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.720A pdb=" N GLY C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.710A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.526A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.284A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.975A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.557A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.546A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.777A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.559A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.810A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.366A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 98 through 103 removed outlier: 7.297A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.967A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.708A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 153 through 161 removed outlier: 3.832A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 217 through 227 removed outlier: 3.531A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.544A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.639A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.202A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.206A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 412 through 424 Processing helix chain 'G' and resid 17 through 27 removed outlier: 4.096A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 97 removed outlier: 3.758A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.894A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 removed outlier: 3.876A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN H 243 " --> pdb=" O ASN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 336 removed outlier: 4.130A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.134A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.133A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.587A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.099A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.244A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.216A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.825A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.730A pdb=" N ILE F 465 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 160 Processing sheet with id=AB3, first strand: chain 'F' and resid 406 through 411 removed outlier: 4.401A pdb=" N LEU F 281 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER G 69 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 79 through 85 removed outlier: 7.081A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 42 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY G 45 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.590A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.995A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 289 removed outlier: 3.507A pdb=" N SER H 262 " --> pdb=" O GLU H 255 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6893 1.36 - 1.50: 5704 1.50 - 1.65: 8957 1.65 - 1.80: 78 1.80 - 1.95: 90 Bond restraints: 21722 Sorted by residual: bond pdb=" N GLN D 25 " pdb=" CA GLN D 25 " ideal model delta sigma weight residual 1.455 1.487 -0.033 9.60e-03 1.09e+04 1.16e+01 bond pdb=" CG1 ILE H 335 " pdb=" CD1 ILE H 335 " ideal model delta sigma weight residual 1.513 1.390 0.123 3.90e-02 6.57e+02 9.96e+00 bond pdb=" N ILE F 121 " pdb=" CA ILE F 121 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.40e+00 bond pdb=" C3' DC J 13 " pdb=" C2' DC J 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" N VAL F 7 " pdb=" CA VAL F 7 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.19e-02 7.06e+03 9.24e+00 ... (remaining 21717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 28368 1.63 - 3.26: 983 3.26 - 4.89: 135 4.89 - 6.52: 12 6.52 - 8.15: 3 Bond angle restraints: 29501 Sorted by residual: angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" C LYS D 30 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" O4 DT K 7 " pdb=" C4 DT K 7 " pdb=" C5 DT K 7 " ideal model delta sigma weight residual 124.90 121.80 3.10 7.00e-01 2.04e+00 1.96e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT K 9 " pdb=" C4 DT K 9 " pdb=" O4 DT K 9 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 29496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 12460 35.46 - 70.91: 619 70.91 - 106.37: 27 106.37 - 141.82: 1 141.82 - 177.28: 2 Dihedral angle restraints: 13109 sinusoidal: 5669 harmonic: 7440 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 117.28 -177.28 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 85.27 -145.27 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 61.01 -121.01 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 13106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3222 0.105 - 0.210: 196 0.210 - 0.314: 1 0.314 - 0.419: 0 0.419 - 0.524: 1 Chirality restraints: 3420 Sorted by residual: chirality pdb=" P DT I 34 " pdb=" OP1 DT I 34 " pdb=" OP2 DT I 34 " pdb=" O5' DT I 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" CA ILE F 121 " pdb=" N ILE F 121 " pdb=" C ILE F 121 " pdb=" CB ILE F 121 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE G 304 " pdb=" N ILE G 304 " pdb=" C ILE G 304 " pdb=" CB ILE G 304 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 3417 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO H 337 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 470 " 0.186 9.50e-02 1.11e+02 8.36e-02 4.28e+00 pdb=" NE ARG F 470 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 470 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 224 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C GLU C 224 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU C 224 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP C 225 " 0.012 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 73 2.45 - 3.06: 13992 3.06 - 3.67: 32655 3.67 - 4.29: 49372 4.29 - 4.90: 82708 Nonbonded interactions: 178800 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.835 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 1.899 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 1.907 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.093 2.170 nonbonded pdb=" OE1 GLU B 301 " pdb=" OH TYR C 308 " model vdw 2.201 3.040 ... (remaining 178795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 21722 Z= 0.289 Angle : 0.670 8.148 29501 Z= 0.424 Chirality : 0.048 0.524 3420 Planarity : 0.004 0.084 3557 Dihedral : 18.390 177.279 8249 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.69 % Allowed : 27.31 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2469 helix: 0.53 (0.16), residues: 1214 sheet: -0.21 (0.25), residues: 504 loop : -1.02 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.018 0.001 TYR G 181 PHE 0.012 0.001 PHE H 66 TRP 0.009 0.001 TRP A 66 HIS 0.011 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.29 (21722) covalent geometry : angle 0.66967 / 0.42 (29501) hydrogen bonds : bond 0.18212 / 11.99 ( 1103) hydrogen bonds : angle 6.86122 / 5.01 ( 3115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.4205 (tpt) cc_final: 0.3260 (mtt) REVERT: B 145 ASN cc_start: 0.8774 (m-40) cc_final: 0.8471 (m-40) REVERT: C 104 ARG cc_start: 0.6938 (ttp80) cc_final: 0.6738 (mtp85) REVERT: F 472 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7625 (tttp) REVERT: G 64 ARG cc_start: 0.7164 (ttm170) cc_final: 0.6641 (mtp180) REVERT: G 151 ARG cc_start: 0.6231 (tpp-160) cc_final: 0.4979 (tpt170) outliers start: 62 outliers final: 54 residues processed: 303 average time/residue: 0.5453 time to fit residues: 191.2764 Evaluate side-chains 281 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 366 ASN A 411 ASN A 436 HIS C 333 ASN D 311 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 243 ASN E 244 ASN F 8 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.211106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.155533 restraints weight = 24073.125| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.28 r_work: 0.3594 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21722 Z= 0.191 Angle : 0.631 7.725 29501 Z= 0.334 Chirality : 0.045 0.210 3420 Planarity : 0.004 0.063 3557 Dihedral : 14.794 158.555 3263 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.39 % Allowed : 24.01 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2469 helix: 0.63 (0.15), residues: 1213 sheet: -0.09 (0.24), residues: 500 loop : -0.79 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 62 TYR 0.015 0.002 TYR F 80 PHE 0.019 0.002 PHE H 66 TRP 0.013 0.001 TRP H 42 HIS 0.007 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (21722) covalent geometry : angle 0.63100 / 0.33 (29501) hydrogen bonds : bond 0.05124 / 3.34 ( 1103) hydrogen bonds : angle 5.25119 / 3.82 ( 3115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 271 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7059 (t) cc_final: 0.6409 (p) REVERT: A 273 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6812 (mp) REVERT: C 39 LYS cc_start: 0.7429 (mtpp) cc_final: 0.6971 (ttmt) REVERT: C 86 ASP cc_start: 0.8488 (m-30) cc_final: 0.8079 (m-30) REVERT: C 234 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7686 (mt-10) REVERT: D 123 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7249 (mttt) REVERT: E 212 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6169 (tt0) REVERT: E 220 LYS cc_start: 0.7883 (tppp) cc_final: 0.7189 (mppt) REVERT: E 314 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7909 (p0) REVERT: F 472 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7496 (tttp) REVERT: G 151 ARG cc_start: 0.5885 (tpp-160) cc_final: 0.4605 (tpt170) REVERT: G 254 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.4592 (mtpp) outliers start: 101 outliers final: 44 residues processed: 339 average time/residue: 0.5521 time to fit residues: 216.1386 Evaluate side-chains 280 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 247 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 ASN A 411 ASN B 8 GLN C 298 HIS E 104 ASN E 144 ASN F 406 HIS G 143 ASN G 190 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.211241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157252 restraints weight = 24212.038| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.38 r_work: 0.3585 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 21722 Z= 0.144 Angle : 0.565 10.001 29501 Z= 0.298 Chirality : 0.042 0.219 3420 Planarity : 0.004 0.056 3557 Dihedral : 14.467 146.485 3197 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 24.53 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2469 helix: 0.88 (0.15), residues: 1208 sheet: -0.15 (0.23), residues: 509 loop : -0.71 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 106 TYR 0.027 0.001 TYR C 71 PHE 0.032 0.002 PHE H 324 TRP 0.027 0.001 TRP H 42 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (21722) covalent geometry : angle 0.56461 / 0.30 (29501) hydrogen bonds : bond 0.04364 / 2.86 ( 1103) hydrogen bonds : angle 4.85472 / 3.54 ( 3115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 255 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7063 (t) cc_final: 0.6396 (p) REVERT: A 77 GLN cc_start: 0.7301 (mt0) cc_final: 0.6986 (mt0) REVERT: A 163 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6974 (mtp) REVERT: A 178 MET cc_start: 0.3983 (tpt) cc_final: 0.3074 (mtt) REVERT: A 234 ASN cc_start: 0.4895 (OUTLIER) cc_final: 0.4161 (m110) REVERT: A 285 MET cc_start: 0.5550 (OUTLIER) cc_final: 0.5103 (ttp) REVERT: C 39 LYS cc_start: 0.7389 (mtpp) cc_final: 0.6910 (ttmt) REVERT: C 197 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7325 (tt) REVERT: C 234 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7723 (mt-10) REVERT: C 293 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 153 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7322 (mp) REVERT: E 96 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6880 (pt) REVERT: E 97 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6820 (t) REVERT: E 212 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6240 (tt0) REVERT: F 472 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7615 (tttp) REVERT: G 151 ARG cc_start: 0.5962 (tpp-160) cc_final: 0.4758 (tpt170) REVERT: G 176 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6894 (pttt) REVERT: G 189 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4926 (mp0) REVERT: H 236 LEU cc_start: 0.6461 (mp) cc_final: 0.6204 (pp) outliers start: 96 outliers final: 34 residues processed: 321 average time/residue: 0.4830 time to fit residues: 180.2346 Evaluate side-chains 272 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain H residue 20 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 23 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 190 optimal weight: 0.0020 chunk 134 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN B 35 GLN B 98 GLN C 74 ASN C 292 ASN C 333 ASN D 352 GLN E 144 ASN E 336 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.208525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154109 restraints weight = 24129.451| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.31 r_work: 0.3554 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21722 Z= 0.161 Angle : 0.579 7.718 29501 Z= 0.303 Chirality : 0.043 0.232 3420 Planarity : 0.004 0.053 3557 Dihedral : 14.436 157.190 3192 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.12 % Allowed : 24.06 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2469 helix: 0.99 (0.15), residues: 1199 sheet: -0.19 (0.23), residues: 510 loop : -0.70 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.036 0.001 TYR C 71 PHE 0.018 0.002 PHE H 17 TRP 0.018 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (21722) covalent geometry : angle 0.57856 / 0.30 (29501) hydrogen bonds : bond 0.04231 / 2.77 ( 1103) hydrogen bonds : angle 4.70446 / 3.44 ( 3115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 251 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7054 (t) cc_final: 0.6394 (p) REVERT: A 77 GLN cc_start: 0.7400 (mt0) cc_final: 0.7113 (mt0) REVERT: A 163 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6965 (mtp) REVERT: A 285 MET cc_start: 0.5487 (ttp) cc_final: 0.5092 (ttp) REVERT: C 39 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6778 (ttmt) REVERT: C 77 ASN cc_start: 0.7913 (t0) cc_final: 0.7454 (t0) REVERT: C 197 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7399 (tt) REVERT: C 293 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 40 THR cc_start: 0.8901 (p) cc_final: 0.8658 (t) REVERT: E 96 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6769 (pt) REVERT: E 212 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6347 (tt0) REVERT: E 220 LYS cc_start: 0.7761 (tppp) cc_final: 0.7035 (mppt) REVERT: F 209 VAL cc_start: 0.2699 (OUTLIER) cc_final: 0.2334 (m) REVERT: F 264 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6093 (mp) REVERT: F 472 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7497 (tttp) REVERT: G 51 GLU cc_start: 0.7788 (tt0) cc_final: 0.7496 (tp30) REVERT: G 176 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6893 (pttt) REVERT: H 91 LEU cc_start: 0.1215 (OUTLIER) cc_final: 0.0315 (mm) REVERT: H 236 LEU cc_start: 0.6452 (mp) cc_final: 0.6221 (pp) outliers start: 118 outliers final: 54 residues processed: 334 average time/residue: 0.4724 time to fit residues: 183.8464 Evaluate side-chains 293 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 245 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.207892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153875 restraints weight = 24123.321| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.41 r_work: 0.3540 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21722 Z= 0.153 Angle : 0.569 11.077 29501 Z= 0.296 Chirality : 0.043 0.264 3420 Planarity : 0.004 0.057 3557 Dihedral : 14.376 166.670 3185 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.56 % Allowed : 25.18 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2469 helix: 1.10 (0.15), residues: 1200 sheet: -0.16 (0.23), residues: 508 loop : -0.70 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.031 0.001 TYR C 71 PHE 0.014 0.001 PHE H 17 TRP 0.019 0.001 TRP H 42 HIS 0.006 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21722) covalent geometry : angle 0.56912 / 0.30 (29501) hydrogen bonds : bond 0.04038 / 2.66 ( 1103) hydrogen bonds : angle 4.58222 / 3.35 ( 3115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 244 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7036 (t) cc_final: 0.6354 (p) REVERT: A 77 GLN cc_start: 0.7404 (mt0) cc_final: 0.7145 (mt0) REVERT: A 163 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7039 (mtp) REVERT: A 178 MET cc_start: 0.3602 (tpt) cc_final: 0.2799 (mtt) REVERT: A 225 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7481 (mp0) REVERT: A 256 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6512 (mpt) REVERT: A 285 MET cc_start: 0.5422 (ttp) cc_final: 0.5019 (ttp) REVERT: C 39 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6865 (ttmt) REVERT: C 77 ASN cc_start: 0.7943 (t0) cc_final: 0.7445 (t0) REVERT: C 104 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6126 (ttm110) REVERT: C 197 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7371 (tt) REVERT: C 207 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6956 (tpt170) REVERT: C 293 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 40 THR cc_start: 0.8814 (p) cc_final: 0.8567 (t) REVERT: D 311 ASN cc_start: 0.8145 (t0) cc_final: 0.7849 (t0) REVERT: E 96 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6741 (pt) REVERT: E 97 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6786 (t) REVERT: E 212 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: E 220 LYS cc_start: 0.7846 (tppp) cc_final: 0.7159 (mppt) REVERT: F 264 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.6041 (mt) REVERT: F 407 GLU cc_start: 0.6629 (mt-10) cc_final: 0.5997 (mt-10) REVERT: F 472 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7596 (tttp) REVERT: G 51 GLU cc_start: 0.7788 (tt0) cc_final: 0.7496 (tp30) REVERT: G 176 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6823 (ptmt) REVERT: H 91 LEU cc_start: 0.1378 (OUTLIER) cc_final: 0.0481 (mm) REVERT: H 236 LEU cc_start: 0.6422 (mp) cc_final: 0.6198 (pp) outliers start: 105 outliers final: 55 residues processed: 317 average time/residue: 0.5305 time to fit residues: 194.5965 Evaluate side-chains 298 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 231 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 209 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 85 optimal weight: 0.0010 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 HIS B 146 GLN C 298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.209015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154630 restraints weight = 24023.100| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.39 r_work: 0.3567 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21722 Z= 0.119 Angle : 0.549 11.278 29501 Z= 0.284 Chirality : 0.042 0.279 3420 Planarity : 0.004 0.093 3557 Dihedral : 14.335 174.343 3185 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.86 % Allowed : 26.27 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2469 helix: 1.30 (0.15), residues: 1198 sheet: -0.11 (0.23), residues: 503 loop : -0.58 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.031 0.001 TYR C 71 PHE 0.036 0.001 PHE H 324 TRP 0.017 0.001 TRP H 42 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21722) covalent geometry : angle 0.54937 / 0.28 (29501) hydrogen bonds : bond 0.03698 / 2.44 ( 1103) hydrogen bonds : angle 4.45957 / 3.27 ( 3115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 244 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7089 (t) cc_final: 0.6319 (p) REVERT: A 77 GLN cc_start: 0.7376 (mt0) cc_final: 0.7070 (mt0) REVERT: A 163 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6955 (mtp) REVERT: A 178 MET cc_start: 0.3794 (tpt) cc_final: 0.2885 (mtt) REVERT: A 223 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 225 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7660 (mp0) REVERT: A 256 MET cc_start: 0.6808 (mpt) cc_final: 0.6489 (mpt) REVERT: A 285 MET cc_start: 0.5450 (ttp) cc_final: 0.5071 (ttp) REVERT: A 403 CYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6835 (m) REVERT: B 50 MET cc_start: 0.6783 (ppp) cc_final: 0.6510 (ppp) REVERT: C 39 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6934 (ttmt) REVERT: C 77 ASN cc_start: 0.7894 (t0) cc_final: 0.7483 (t0) REVERT: C 104 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.5773 (ttm110) REVERT: C 197 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7344 (tt) REVERT: D 40 THR cc_start: 0.8796 (p) cc_final: 0.8507 (t) REVERT: E 96 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6699 (pt) REVERT: E 97 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6651 (t) REVERT: E 212 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: E 220 LYS cc_start: 0.7886 (tppp) cc_final: 0.7172 (mppt) REVERT: F 93 MET cc_start: 0.3769 (mpp) cc_final: 0.3548 (mpp) REVERT: F 209 VAL cc_start: 0.2634 (OUTLIER) cc_final: 0.2399 (m) REVERT: F 231 MET cc_start: 0.5090 (tpp) cc_final: 0.3819 (ptm) REVERT: F 264 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6257 (mt) REVERT: F 472 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7666 (tttp) REVERT: G 51 GLU cc_start: 0.7843 (tt0) cc_final: 0.7419 (tp30) REVERT: G 176 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6683 (ptmt) REVERT: G 250 LYS cc_start: 0.7214 (tttp) cc_final: 0.6780 (tmtt) REVERT: H 236 LEU cc_start: 0.6447 (mp) cc_final: 0.6213 (pp) outliers start: 89 outliers final: 53 residues processed: 310 average time/residue: 0.5089 time to fit residues: 182.0830 Evaluate side-chains 293 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 184 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 249 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.208534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154798 restraints weight = 24063.294| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.38 r_work: 0.3546 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21722 Z= 0.137 Angle : 0.556 9.877 29501 Z= 0.287 Chirality : 0.042 0.212 3420 Planarity : 0.004 0.091 3557 Dihedral : 14.278 171.075 3185 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.26 % Allowed : 26.44 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2469 helix: 1.29 (0.15), residues: 1198 sheet: -0.10 (0.23), residues: 503 loop : -0.56 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 68 TYR 0.036 0.001 TYR C 71 PHE 0.029 0.001 PHE H 17 TRP 0.015 0.001 TRP H 42 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21722) covalent geometry : angle 0.55646 / 0.29 (29501) hydrogen bonds : bond 0.03786 / 2.50 ( 1103) hydrogen bonds : angle 4.42824 / 3.23 ( 3115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 243 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7034 (t) cc_final: 0.6465 (t) REVERT: A 77 GLN cc_start: 0.7415 (mt0) cc_final: 0.7214 (mt0) REVERT: A 107 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6778 (mp) REVERT: A 163 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6841 (mtp) REVERT: A 225 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 250 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6333 (mmm) REVERT: A 256 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6487 (mpt) REVERT: A 403 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6691 (m) REVERT: B 50 MET cc_start: 0.6734 (ppp) cc_final: 0.6439 (ppp) REVERT: C 39 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6862 (ttmt) REVERT: C 77 ASN cc_start: 0.7856 (t0) cc_final: 0.7502 (t0) REVERT: C 197 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7348 (tt) REVERT: C 207 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6931 (tpt170) REVERT: D 40 THR cc_start: 0.8788 (p) cc_final: 0.8526 (t) REVERT: E 96 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6679 (pt) REVERT: E 97 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6726 (t) REVERT: E 212 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: E 220 LYS cc_start: 0.7820 (tppp) cc_final: 0.7157 (mppt) REVERT: F 264 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6082 (mp) REVERT: F 407 GLU cc_start: 0.6569 (mt-10) cc_final: 0.5929 (mt-10) REVERT: F 426 GLU cc_start: 0.4405 (OUTLIER) cc_final: 0.3767 (mp0) REVERT: F 472 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7538 (tttp) REVERT: G 51 GLU cc_start: 0.7774 (tt0) cc_final: 0.7414 (tp30) REVERT: G 176 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6726 (ptmt) REVERT: G 250 LYS cc_start: 0.7185 (tttp) cc_final: 0.6744 (tmtt) REVERT: H 236 LEU cc_start: 0.6448 (mp) cc_final: 0.6212 (pp) outliers start: 98 outliers final: 55 residues processed: 314 average time/residue: 0.4947 time to fit residues: 179.9783 Evaluate side-chains 303 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 241 optimal weight: 20.0000 chunk 171 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN G 164 HIS H 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.208404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154305 restraints weight = 24142.482| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.31 r_work: 0.3559 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21722 Z= 0.128 Angle : 0.558 12.614 29501 Z= 0.287 Chirality : 0.042 0.278 3420 Planarity : 0.004 0.087 3557 Dihedral : 14.181 155.098 3184 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.04 % Allowed : 27.05 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2469 helix: 1.36 (0.15), residues: 1198 sheet: 0.01 (0.24), residues: 497 loop : -0.54 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 68 TYR 0.034 0.001 TYR C 71 PHE 0.037 0.001 PHE H 324 TRP 0.015 0.001 TRP H 42 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21722) covalent geometry : angle 0.55791 / 0.29 (29501) hydrogen bonds : bond 0.03640 / 2.41 ( 1103) hydrogen bonds : angle 4.35920 / 3.19 ( 3115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 246 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7023 (t) cc_final: 0.6411 (t) REVERT: A 77 GLN cc_start: 0.7430 (mt0) cc_final: 0.7209 (mt0) REVERT: A 107 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6897 (mp) REVERT: A 152 ARG cc_start: 0.5269 (OUTLIER) cc_final: 0.4693 (mtp85) REVERT: A 163 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6907 (mtp) REVERT: A 178 MET cc_start: 0.3591 (tpt) cc_final: 0.3008 (mtt) REVERT: A 223 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 250 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.6398 (mmm) REVERT: A 256 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6582 (mpt) REVERT: A 403 CYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6855 (m) REVERT: B 50 MET cc_start: 0.6843 (ppp) cc_final: 0.6559 (ppp) REVERT: B 149 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8344 (mmtm) REVERT: C 39 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6896 (ttmt) REVERT: C 77 ASN cc_start: 0.7909 (t0) cc_final: 0.7560 (t0) REVERT: C 197 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7364 (tt) REVERT: D 40 THR cc_start: 0.8817 (p) cc_final: 0.8504 (t) REVERT: E 96 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6668 (pt) REVERT: E 97 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6736 (t) REVERT: E 212 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: F 93 MET cc_start: 0.3605 (mpp) cc_final: 0.2139 (mtm) REVERT: F 264 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6238 (mp) REVERT: F 472 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7742 (tttp) REVERT: G 51 GLU cc_start: 0.7818 (tt0) cc_final: 0.7474 (tp30) REVERT: G 176 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6563 (ptmt) REVERT: G 250 LYS cc_start: 0.7159 (tttp) cc_final: 0.6736 (tmtt) REVERT: H 236 LEU cc_start: 0.6447 (mp) cc_final: 0.6203 (pp) REVERT: H 284 MET cc_start: 0.4196 (mmt) cc_final: 0.3526 (tpt) outliers start: 93 outliers final: 52 residues processed: 314 average time/residue: 0.5701 time to fit residues: 207.3542 Evaluate side-chains 302 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 324 PHE Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 26 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 113 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.207931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153985 restraints weight = 24115.343| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.39 r_work: 0.3551 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21722 Z= 0.137 Angle : 0.573 11.672 29501 Z= 0.292 Chirality : 0.043 0.249 3420 Planarity : 0.004 0.091 3557 Dihedral : 14.161 145.919 3183 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.43 % Allowed : 27.70 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2469 helix: 1.33 (0.15), residues: 1199 sheet: 0.03 (0.24), residues: 499 loop : -0.52 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 68 TYR 0.030 0.001 TYR C 71 PHE 0.031 0.001 PHE H 17 TRP 0.014 0.001 TRP H 42 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21722) covalent geometry : angle 0.57332 / 0.29 (29501) hydrogen bonds : bond 0.03692 / 2.44 ( 1103) hydrogen bonds : angle 4.35483 / 3.18 ( 3115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 246 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7064 (t) cc_final: 0.6449 (t) REVERT: A 77 GLN cc_start: 0.7436 (mt0) cc_final: 0.7216 (mt0) REVERT: A 152 ARG cc_start: 0.5349 (OUTLIER) cc_final: 0.4781 (mtp85) REVERT: A 163 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: A 178 MET cc_start: 0.3638 (tpt) cc_final: 0.3039 (mtt) REVERT: A 250 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6381 (mmm) REVERT: A 256 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6604 (mpt) REVERT: A 403 CYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6894 (m) REVERT: B 50 MET cc_start: 0.6877 (ppp) cc_final: 0.6586 (ppp) REVERT: B 149 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8357 (mmtm) REVERT: C 39 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6947 (ttmt) REVERT: C 77 ASN cc_start: 0.7955 (t0) cc_final: 0.7610 (t0) REVERT: C 197 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7362 (tt) REVERT: C 207 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7163 (tpt170) REVERT: D 40 THR cc_start: 0.8815 (p) cc_final: 0.8496 (t) REVERT: E 96 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6622 (pt) REVERT: E 212 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: E 343 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8068 (tt0) REVERT: F 1 MET cc_start: -0.0528 (ptm) cc_final: -0.0810 (ttp) REVERT: F 93 MET cc_start: 0.3696 (mpp) cc_final: 0.2278 (mtm) REVERT: F 264 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6219 (mp) REVERT: F 407 GLU cc_start: 0.6660 (mt-10) cc_final: 0.5989 (mt-10) REVERT: F 472 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7728 (tttp) REVERT: G 51 GLU cc_start: 0.7830 (tt0) cc_final: 0.7488 (tp30) REVERT: G 176 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6568 (ptmt) REVERT: G 250 LYS cc_start: 0.7058 (tttp) cc_final: 0.6636 (tmtt) REVERT: H 236 LEU cc_start: 0.6447 (mp) cc_final: 0.6205 (pp) REVERT: H 284 MET cc_start: 0.4172 (mmt) cc_final: 0.3503 (tpt) outliers start: 79 outliers final: 55 residues processed: 305 average time/residue: 0.5400 time to fit residues: 190.1596 Evaluate side-chains 307 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 0.0000 chunk 126 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.207393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153781 restraints weight = 24294.513| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.37 r_work: 0.3551 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21722 Z= 0.146 Angle : 0.590 11.608 29501 Z= 0.301 Chirality : 0.043 0.243 3420 Planarity : 0.004 0.074 3557 Dihedral : 14.142 133.019 3183 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.39 % Allowed : 27.83 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2469 helix: 1.29 (0.15), residues: 1198 sheet: 0.05 (0.23), residues: 503 loop : -0.52 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 106 TYR 0.044 0.001 TYR F 107 PHE 0.031 0.001 PHE A 279 TRP 0.013 0.001 TRP H 42 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (21722) covalent geometry : angle 0.59026 / 0.30 (29501) hydrogen bonds : bond 0.03740 / 2.47 ( 1103) hydrogen bonds : angle 4.35982 / 3.18 ( 3115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 242 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7066 (t) cc_final: 0.6437 (t) REVERT: A 77 GLN cc_start: 0.7450 (mt0) cc_final: 0.7244 (mt0) REVERT: A 105 LEU cc_start: 0.6263 (tt) cc_final: 0.5973 (tp) REVERT: A 152 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4994 (mtp85) REVERT: A 163 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: A 178 MET cc_start: 0.3544 (tpt) cc_final: 0.2971 (mtt) REVERT: A 256 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6597 (mpt) REVERT: A 403 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6760 (m) REVERT: B 50 MET cc_start: 0.6800 (ppp) cc_final: 0.6521 (ppp) REVERT: B 149 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8310 (mmtm) REVERT: C 39 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6865 (ttmt) REVERT: C 77 ASN cc_start: 0.7895 (t0) cc_final: 0.7607 (t0) REVERT: C 197 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7358 (tt) REVERT: C 207 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6933 (tpt170) REVERT: C 286 GLU cc_start: 0.7943 (tp30) cc_final: 0.7705 (tp30) REVERT: D 40 THR cc_start: 0.8799 (p) cc_final: 0.8516 (t) REVERT: E 96 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6644 (pt) REVERT: E 97 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6759 (t) REVERT: E 212 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: E 220 LYS cc_start: 0.7863 (tppp) cc_final: 0.7187 (mppt) REVERT: E 343 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7890 (tt0) REVERT: F 1 MET cc_start: -0.0517 (ptm) cc_final: -0.0788 (ttp) REVERT: F 93 MET cc_start: 0.3704 (mpp) cc_final: 0.2315 (mtm) REVERT: F 264 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6041 (mp) REVERT: F 407 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5940 (mt-10) REVERT: F 472 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7609 (tttp) REVERT: G 176 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6603 (ptmt) REVERT: G 250 LYS cc_start: 0.7092 (tttp) cc_final: 0.6676 (tmtt) REVERT: H 236 LEU cc_start: 0.6442 (mp) cc_final: 0.6207 (pp) REVERT: H 284 MET cc_start: 0.4309 (mmt) cc_final: 0.3571 (tpt) outliers start: 78 outliers final: 53 residues processed: 303 average time/residue: 0.5283 time to fit residues: 185.4602 Evaluate side-chains 303 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN C 140 ASN F 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.204992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150620 restraints weight = 24282.266| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.47 r_work: 0.3528 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21722 Z= 0.155 Angle : 0.601 11.572 29501 Z= 0.305 Chirality : 0.043 0.236 3420 Planarity : 0.004 0.067 3557 Dihedral : 14.139 118.149 3183 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.91 % Allowed : 28.18 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2469 helix: 1.21 (0.15), residues: 1204 sheet: 0.03 (0.23), residues: 503 loop : -0.58 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 106 TYR 0.039 0.001 TYR F 107 PHE 0.042 0.002 PHE H 324 TRP 0.013 0.001 TRP H 42 HIS 0.006 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (21722) covalent geometry : angle 0.60115 / 0.30 (29501) hydrogen bonds : bond 0.03837 / 2.55 ( 1103) hydrogen bonds : angle 4.37751 / 3.19 ( 3115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7517.51 seconds wall clock time: 128 minutes 55.69 seconds (7735.69 seconds total)