Starting phenix.real_space_refine on Fri Mar 6 00:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.map" model { file = "/net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ly8_30014/03_2026/6ly8_30014.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 101 5.16 5 C 16918 2.51 5 N 4595 2.21 5 O 5015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26631 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.22 Number of scatterers: 26631 At special positions: 0 Unit cell: (139.7, 129.8, 162.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 2 15.00 O 5015 8.00 N 4595 7.00 C 16918 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6214 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 37 sheets defined 41.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 267 removed outlier: 4.608A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.638A pdb=" N HIS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.207A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.727A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.634A pdb=" N ARG A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 471 removed outlier: 5.098A pdb=" N GLY A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 533 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.898A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.908A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.771A pdb=" N THR B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.513A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 285 " --> pdb=" O MET B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 316 Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.754A pdb=" N LEU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 446 through 472 removed outlier: 5.073A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 removed outlier: 3.709A pdb=" N ARG B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 558 through 574 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.078A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.941A pdb=" N THR C 285 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.748A pdb=" N GLY C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.992A pdb=" N TYR C 350 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.914A pdb=" N ASP C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.842A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.509A pdb=" N GLU D 184 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 185 " --> pdb=" O GLU D 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 181 through 185' Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.546A pdb=" N LEU D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.814A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.751A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.826A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 374 through 400 removed outlier: 4.267A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 445 removed outlier: 4.012A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 462 removed outlier: 4.227A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.445A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.904A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.553A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.535A pdb=" N ARG E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 399 Processing helix chain 'E' and resid 400 through 404 removed outlier: 4.469A pdb=" N ALA E 403 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU E 404 " --> pdb=" O GLU E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 404' Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.554A pdb=" N TYR E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 462 removed outlier: 3.711A pdb=" N ILE E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.780A pdb=" N VAL F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 175 through 178 removed outlier: 3.582A pdb=" N SER F 178 " --> pdb=" O PRO F 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.564A pdb=" N LEU F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 248 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 275 removed outlier: 3.918A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.685A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 removed outlier: 3.649A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'G' and resid 9 through 65 removed outlier: 4.036A pdb=" N GLN G 13 " --> pdb=" O MET G 9 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET G 47 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.524A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 121 through 206 removed outlier: 3.902A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.862A pdb=" N GLU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 15 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'H' and resid 83 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.243A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 21 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.536A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 removed outlier: 4.133A pdb=" N VAL A 129 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.077A pdb=" N ILE A 226 " --> pdb=" O VAL A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.687A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 251 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 379 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.668A pdb=" N VAL B 65 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 47 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 45 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 33 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE E 32 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.669A pdb=" N ILE B 147 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'B' and resid 197 through 198 removed outlier: 4.135A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 369 " --> pdb=" O ARG B 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.601A pdb=" N VAL B 384 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 379 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 324 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 10 removed outlier: 6.725A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.741A pdb=" N GLU C 140 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.622A pdb=" N VAL C 129 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.636A pdb=" N GLU C 159 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 197 through 198 removed outlier: 3.949A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.630A pdb=" N ILE C 226 " --> pdb=" O GLY C 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 32 through 36 removed outlier: 6.901A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.536A pdb=" N VAL D 84 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.727A pdb=" N LYS D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA D 192 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.712A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AC8, first strand: chain 'D' and resid 252 through 255 removed outlier: 3.553A pdb=" N THR D 309 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 336 through 339 removed outlier: 9.895A pdb=" N GLN D 336 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N LEU D 355 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLN D 338 " --> pdb=" O ASP D 353 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.747A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 15 removed outlier: 4.240A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER F 15 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 19 " --> pdb=" O ILE F 57 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 42 through 44 removed outlier: 6.978A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.509A pdb=" N LEU F 112 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.534A pdb=" N LYS F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA F 192 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.521A pdb=" N THR F 172 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 313 through 315 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.473A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 309 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 4 removed outlier: 6.426A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8889 1.34 - 1.45: 3067 1.45 - 1.57: 15004 1.57 - 1.69: 3 1.69 - 1.80: 190 Bond restraints: 27153 Sorted by residual: bond pdb=" N ILE E 459 " pdb=" CA ILE E 459 " ideal model delta sigma weight residual 1.461 1.435 0.026 1.19e-02 7.06e+03 4.62e+00 bond pdb=" N ILE D 459 " pdb=" CA ILE D 459 " ideal model delta sigma weight residual 1.461 1.441 0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" C HIS D 458 " pdb=" N ILE D 459 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.26e-02 6.30e+03 2.20e+00 bond pdb=" C ILE F 459 " pdb=" O ILE F 459 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.17e-02 7.31e+03 2.05e+00 bond pdb=" N GLY F 299 " pdb=" CA GLY F 299 " ideal model delta sigma weight residual 1.453 1.441 0.012 8.60e-03 1.35e+04 1.90e+00 ... (remaining 27148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 36040 1.99 - 3.98: 670 3.98 - 5.96: 69 5.96 - 7.95: 13 7.95 - 9.94: 1 Bond angle restraints: 36793 Sorted by residual: angle pdb=" N ILE E 459 " pdb=" CA ILE E 459 " pdb=" C ILE E 459 " ideal model delta sigma weight residual 110.62 105.55 5.07 1.02e+00 9.61e-01 2.47e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.08 -7.27 2.21e+00 2.05e-01 1.08e+01 angle pdb=" N GLU E 276 " pdb=" CA GLU E 276 " pdb=" C GLU E 276 " ideal model delta sigma weight residual 110.44 114.37 -3.93 1.20e+00 6.94e-01 1.07e+01 angle pdb=" C ASN B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 122.97 120.00 2.97 9.80e-01 1.04e+00 9.19e+00 angle pdb=" C GLY E 179 " pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.41e+00 ... (remaining 36788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 15692 27.67 - 55.34: 712 55.34 - 83.01: 74 83.01 - 110.68: 15 110.68 - 138.35: 1 Dihedral angle restraints: 16494 sinusoidal: 6744 harmonic: 9750 Sorted by residual: dihedral pdb=" CA PHE C 419 " pdb=" C PHE C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta harmonic sigma weight residual 180.00 -103.55 -76.45 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" C5' ADP A 600 " pdb=" O5' ADP A 600 " pdb=" PA ADP A 600 " pdb=" O2A ADP A 600 " ideal model delta sinusoidal sigma weight residual 300.00 161.66 138.35 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" CA THR B 273 " pdb=" C THR B 273 " pdb=" N ASP B 274 " pdb=" CA ASP B 274 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 16491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2352 0.034 - 0.068: 1207 0.068 - 0.103: 374 0.103 - 0.137: 164 0.137 - 0.171: 12 Chirality restraints: 4109 Sorted by residual: chirality pdb=" CA PHE C 419 " pdb=" N PHE C 419 " pdb=" C PHE C 419 " pdb=" CB PHE C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE E 459 " pdb=" N ILE E 459 " pdb=" C ILE E 459 " pdb=" CB ILE E 459 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA THR G 119 " pdb=" N THR G 119 " pdb=" C THR G 119 " pdb=" CB THR G 119 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 4106 not shown) Planarity restraints: 4818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 419 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO C 420 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 269 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 270 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 185 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO F 186 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 186 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 186 " -0.032 5.00e-02 4.00e+02 ... (remaining 4815 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 86 2.42 - 3.04: 16801 3.04 - 3.66: 36095 3.66 - 4.28: 52831 4.28 - 4.90: 94186 Nonbonded interactions: 199999 Sorted by model distance: nonbonded pdb=" O ALA C 576 " pdb=" CD2 LEU C 577 " model vdw 1.805 3.460 nonbonded pdb=" O ARG C 547 " pdb=" OH TYR C 562 " model vdw 2.045 3.040 nonbonded pdb=" NH2 ARG C 401 " pdb=" OE2 GLU F 265 " model vdw 2.146 3.120 nonbonded pdb=" NH2 ARG E 91 " pdb=" O PRO E 104 " model vdw 2.148 3.120 nonbonded pdb=" OG SER D 455 " pdb=" OD1 ASP D 457 " model vdw 2.157 3.040 ... (remaining 199994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 577) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.310 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 27154 Z= 0.259 Angle : 0.684 9.940 36793 Z= 0.383 Chirality : 0.047 0.171 4109 Planarity : 0.005 0.097 4818 Dihedral : 15.322 138.345 10280 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.08 % Favored : 88.89 % Rotamer: Outliers : 11.59 % Allowed : 11.84 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -4.29 (0.12), residues: 3402 helix: -1.22 (0.13), residues: 1309 sheet: -3.57 (0.21), residues: 469 loop : -4.13 (0.12), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 314 TYR 0.020 0.002 TYR D 13 PHE 0.019 0.002 PHE C 419 TRP 0.008 0.001 TRP C 117 HIS 0.004 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00612 (27153) covalent geometry : angle 0.68364 (36793) hydrogen bonds : bond 0.15026 ( 1071) hydrogen bonds : angle 6.56982 ( 3117) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 325 poor density : 407 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 24 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.6946 (tmm) REVERT: A 124 LYS cc_start: 0.8442 (tppp) cc_final: 0.7832 (mtpp) REVERT: A 165 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 191 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mtm110) REVERT: A 323 MET cc_start: 0.7585 (ttm) cc_final: 0.7349 (mtp) REVERT: A 410 ASP cc_start: 0.7996 (t0) cc_final: 0.7702 (m-30) REVERT: A 458 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 464 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 541 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: A 574 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: B 157 VAL cc_start: 0.9076 (t) cc_final: 0.8841 (p) REVERT: B 294 MET cc_start: 0.8395 (mtt) cc_final: 0.8159 (mtp) REVERT: B 332 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: B 369 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 423 ASN cc_start: 0.8504 (t0) cc_final: 0.8193 (t0) REVERT: B 509 MET cc_start: 0.7330 (tpt) cc_final: 0.6954 (mmm) REVERT: B 550 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7548 (tpt170) REVERT: B 558 GLU cc_start: 0.7353 (tp30) cc_final: 0.6674 (tp30) REVERT: C 8 LYS cc_start: 0.8928 (tttt) cc_final: 0.8682 (tttm) REVERT: C 130 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7668 (ptt90) REVERT: C 159 GLU cc_start: 0.7492 (tt0) cc_final: 0.7291 (pt0) REVERT: C 266 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (mt) REVERT: C 304 TYR cc_start: 0.8757 (m-80) cc_final: 0.8473 (m-80) REVERT: C 393 GLU cc_start: 0.7646 (tt0) cc_final: 0.7427 (tt0) REVERT: C 538 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.5751 (tm-30) REVERT: C 571 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: D 7 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6216 (pt0) REVERT: D 215 SER cc_start: 0.8757 (m) cc_final: 0.8513 (p) REVERT: D 216 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.6400 (ppt-90) REVERT: D 268 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6952 (ttt180) REVERT: D 381 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7389 (tm130) REVERT: D 392 ILE cc_start: 0.8115 (pt) cc_final: 0.7879 (mt) REVERT: D 442 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (mp) REVERT: D 457 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6781 (p0) REVERT: E 67 ASP cc_start: 0.8122 (t0) cc_final: 0.7768 (t0) REVERT: E 82 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8707 (pt) REVERT: E 130 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8724 (p90) REVERT: E 269 GLU cc_start: 0.7636 (tt0) cc_final: 0.7424 (tt0) REVERT: E 327 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: E 334 GLU cc_start: 0.8302 (pt0) cc_final: 0.8030 (pt0) REVERT: E 368 LYS cc_start: 0.7593 (tptt) cc_final: 0.6659 (tptt) REVERT: E 372 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7418 (mtm110) REVERT: E 373 GLU cc_start: 0.8078 (mp0) cc_final: 0.7647 (mt-10) REVERT: E 394 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7612 (tppt) REVERT: E 401 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 437 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: E 453 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6782 (tpp-160) REVERT: F 111 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7629 (mtm-85) REVERT: F 172 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8687 (p) REVERT: F 327 ASP cc_start: 0.7821 (t70) cc_final: 0.7536 (t0) REVERT: F 331 TYR cc_start: 0.8075 (m-80) cc_final: 0.7627 (m-80) REVERT: F 362 MET cc_start: 0.8877 (ttt) cc_final: 0.8514 (ttt) REVERT: F 410 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.6788 (mtp180) REVERT: F 412 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7484 (mt) REVERT: G 26 ASP cc_start: 0.7817 (m-30) cc_final: 0.7556 (m-30) REVERT: G 44 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6904 (tpt90) REVERT: G 59 GLU cc_start: 0.6882 (tp30) cc_final: 0.6222 (tm-30) REVERT: G 64 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6258 (tp) REVERT: G 135 GLU cc_start: 0.7034 (mp0) cc_final: 0.6613 (mp0) REVERT: G 166 GLN cc_start: 0.7980 (mt0) cc_final: 0.7573 (mt0) REVERT: G 193 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7951 (mtm110) REVERT: G 200 LYS cc_start: 0.7251 (ttmm) cc_final: 0.6926 (mptt) REVERT: H 3 VAL cc_start: 0.5769 (p) cc_final: 0.5461 (t) REVERT: H 77 LEU cc_start: 0.2414 (OUTLIER) cc_final: 0.2106 (tp) REVERT: H 87 GLU cc_start: 0.7515 (tt0) cc_final: 0.7261 (tm-30) REVERT: H 92 GLU cc_start: 0.7699 (pt0) cc_final: 0.7472 (pt0) REVERT: H 96 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.5565 (pttm) outliers start: 325 outliers final: 190 residues processed: 678 average time/residue: 0.1833 time to fit residues: 191.3049 Evaluate side-chains 545 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 325 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 453 ARG Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0020 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 88 GLN A 196 GLN A 496 GLN A 571 GLN B 3 GLN B 7 GLN B 50 GLN B 81 ASN B 88 GLN B 185 HIS ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 496 GLN B 498 ASN C 238 GLN C 316 GLN C 469 GLN C 496 GLN C 497 GLN D 94 ASN D 148 GLN D 161 ASN D 249 HIS D 252 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 336 GLN D 407 ASN D 425 GLN E 166 GLN E 170 GLN E 252 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN E 375 HIS E 427 GLN E 437 GLN E 448 GLN F 46 GLN F 129 GLN F 148 GLN F 252 HIS F 310 GLN F 323 HIS F 363 ASN F 413 GLN F 448 GLN G 17 GLN G 95 ASN G 180 GLN H 11 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101725 restraints weight = 40759.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104486 restraints weight = 23601.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106347 restraints weight = 16338.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107538 restraints weight = 12636.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108433 restraints weight = 10598.325| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27154 Z= 0.121 Angle : 0.573 8.636 36793 Z= 0.296 Chirality : 0.044 0.223 4109 Planarity : 0.005 0.079 4818 Dihedral : 11.132 108.402 4236 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 7.60 % Allowed : 16.76 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.14), residues: 3402 helix: 0.29 (0.15), residues: 1314 sheet: -3.02 (0.21), residues: 507 loop : -3.48 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.012 0.001 TYR A 513 PHE 0.017 0.001 PHE C 419 TRP 0.010 0.001 TRP C 119 HIS 0.004 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00254 (27153) covalent geometry : angle 0.57309 (36793) hydrogen bonds : bond 0.05159 ( 1071) hydrogen bonds : angle 5.12936 ( 3117) Misc. bond : bond 0.00154 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 376 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 8 LYS cc_start: 0.8478 (tttp) cc_final: 0.8186 (tptp) REVERT: A 124 LYS cc_start: 0.8267 (tppp) cc_final: 0.7773 (mtpp) REVERT: A 165 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: A 323 MET cc_start: 0.7139 (ttm) cc_final: 0.6876 (mtp) REVERT: A 458 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8170 (mm) REVERT: A 464 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (mm) REVERT: B 213 ASP cc_start: 0.7840 (t0) cc_final: 0.7619 (t0) REVERT: B 282 MET cc_start: 0.9233 (mmt) cc_final: 0.9024 (tpt) REVERT: B 294 MET cc_start: 0.8048 (mtt) cc_final: 0.7796 (mtp) REVERT: B 296 VAL cc_start: 0.5202 (OUTLIER) cc_final: 0.4438 (m) REVERT: B 423 ASN cc_start: 0.8458 (t0) cc_final: 0.8185 (t0) REVERT: B 558 GLU cc_start: 0.6886 (tp30) cc_final: 0.6468 (tp30) REVERT: C 220 MET cc_start: 0.7989 (tmm) cc_final: 0.7346 (tmm) REVERT: C 266 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8490 (mt) REVERT: C 304 TYR cc_start: 0.8657 (m-80) cc_final: 0.8313 (m-80) REVERT: C 393 GLU cc_start: 0.7496 (tt0) cc_final: 0.7259 (tt0) REVERT: C 527 GLU cc_start: 0.8138 (tp30) cc_final: 0.7893 (tp30) REVERT: C 538 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: D 103 LEU cc_start: 0.8892 (mm) cc_final: 0.8677 (mt) REVERT: D 381 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7096 (tm130) REVERT: D 401 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: D 442 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mp) REVERT: E 111 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8209 (mtp85) REVERT: E 130 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8622 (p90) REVERT: E 321 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7827 (ttt180) REVERT: E 327 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: E 381 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7592 (tp40) REVERT: E 394 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7181 (tppt) REVERT: E 427 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: F 111 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7468 (mtm-85) REVERT: F 185 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5995 (mm-30) REVERT: F 290 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8021 (t0) REVERT: F 362 MET cc_start: 0.8761 (ttt) cc_final: 0.8423 (ttt) REVERT: F 410 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6676 (mtp180) REVERT: G 26 ASP cc_start: 0.7582 (m-30) cc_final: 0.7372 (m-30) REVERT: G 44 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7007 (tpt90) REVERT: G 59 GLU cc_start: 0.6888 (tp30) cc_final: 0.6146 (tm-30) REVERT: G 64 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6192 (tp) REVERT: G 132 ARG cc_start: 0.7570 (mmm160) cc_final: 0.7338 (mmm160) REVERT: G 185 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: G 200 LYS cc_start: 0.7400 (ttmm) cc_final: 0.7068 (mptt) REVERT: H 1 MET cc_start: 0.7193 (mpt) cc_final: 0.6899 (mpt) REVERT: H 77 LEU cc_start: 0.2719 (OUTLIER) cc_final: 0.2403 (tp) REVERT: H 96 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.5403 (pttp) outliers start: 213 outliers final: 124 residues processed: 545 average time/residue: 0.1742 time to fit residues: 149.7829 Evaluate side-chains 458 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 314 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 213 optimal weight: 3.9990 chunk 321 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 333 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN B 418 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 166 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098351 restraints weight = 41476.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101555 restraints weight = 24930.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103244 restraints weight = 15329.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104261 restraints weight = 11842.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104440 restraints weight = 11394.831| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27154 Z= 0.226 Angle : 0.636 8.382 36793 Z= 0.328 Chirality : 0.047 0.270 4109 Planarity : 0.005 0.087 4818 Dihedral : 10.105 97.878 4048 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.76 % Favored : 90.21 % Rotamer: Outliers : 7.56 % Allowed : 18.22 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.14), residues: 3402 helix: 0.56 (0.15), residues: 1313 sheet: -2.77 (0.22), residues: 510 loop : -3.32 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 193 TYR 0.020 0.002 TYR D 13 PHE 0.015 0.002 PHE A 574 TRP 0.012 0.001 TRP C 119 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00549 (27153) covalent geometry : angle 0.63603 (36793) hydrogen bonds : bond 0.06305 ( 1071) hydrogen bonds : angle 5.11224 ( 3117) Misc. bond : bond 0.00198 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 333 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 8 LYS cc_start: 0.8599 (tttp) cc_final: 0.8315 (tptp) REVERT: A 124 LYS cc_start: 0.8433 (tppp) cc_final: 0.7943 (mtpp) REVERT: A 165 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: A 353 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.7574 (p90) REVERT: A 464 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (mm) REVERT: B 88 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8973 (tt0) REVERT: B 282 MET cc_start: 0.9145 (mmt) cc_final: 0.8933 (tpt) REVERT: B 294 MET cc_start: 0.8352 (mtt) cc_final: 0.8104 (mtp) REVERT: B 423 ASN cc_start: 0.8489 (t0) cc_final: 0.8168 (t0) REVERT: B 558 GLU cc_start: 0.7038 (tp30) cc_final: 0.6745 (tp30) REVERT: C 116 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7928 (ptpp) REVERT: C 220 MET cc_start: 0.8159 (tmm) cc_final: 0.7397 (tmm) REVERT: C 266 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8550 (mt) REVERT: C 304 TYR cc_start: 0.8758 (m-80) cc_final: 0.8417 (m-80) REVERT: C 393 GLU cc_start: 0.7577 (tt0) cc_final: 0.7351 (tt0) REVERT: C 538 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: D 270 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8691 (mt) REVERT: D 381 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7238 (tm130) REVERT: D 442 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9073 (mp) REVERT: E 111 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8218 (mtp85) REVERT: E 130 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8713 (p90) REVERT: E 321 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7909 (ttt180) REVERT: E 327 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: E 381 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7871 (tm-30) REVERT: E 394 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7184 (tppt) REVERT: E 427 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: F 111 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7510 (mtm-85) REVERT: F 185 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6094 (mm-30) REVERT: F 290 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (t0) REVERT: F 362 MET cc_start: 0.8834 (ttt) cc_final: 0.8508 (ttt) REVERT: F 406 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6150 (tm-30) REVERT: F 410 ARG cc_start: 0.7366 (mtt-85) cc_final: 0.6871 (mtm-85) REVERT: F 413 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: G 26 ASP cc_start: 0.7635 (m-30) cc_final: 0.7404 (m-30) REVERT: G 44 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7089 (tpt90) REVERT: G 55 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6859 (tm-30) REVERT: G 59 GLU cc_start: 0.7040 (tp30) cc_final: 0.6669 (mm-30) REVERT: G 64 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6620 (tp) REVERT: G 185 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: G 200 LYS cc_start: 0.7486 (ttmm) cc_final: 0.7181 (mptt) REVERT: H 60 GLU cc_start: 0.5164 (tt0) cc_final: 0.4779 (pp20) REVERT: H 87 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7890 (tm-30) REVERT: H 96 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.5467 (pttp) outliers start: 212 outliers final: 157 residues processed: 511 average time/residue: 0.1753 time to fit residues: 140.6768 Evaluate side-chains 481 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 303 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 204 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 326 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 0.0170 chunk 295 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 571 GLN B 283 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102639 restraints weight = 40596.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105449 restraints weight = 23363.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107334 restraints weight = 16018.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108597 restraints weight = 12336.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109409 restraints weight = 10292.445| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27154 Z= 0.107 Angle : 0.539 8.776 36793 Z= 0.276 Chirality : 0.043 0.267 4109 Planarity : 0.005 0.074 4818 Dihedral : 9.461 90.410 4036 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 6.46 % Allowed : 19.37 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 3402 helix: 1.07 (0.15), residues: 1305 sheet: -2.44 (0.23), residues: 484 loop : -2.90 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.009 0.001 TYR A 513 PHE 0.013 0.001 PHE C 419 TRP 0.010 0.001 TRP C 119 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00226 (27153) covalent geometry : angle 0.53909 (36793) hydrogen bonds : bond 0.04453 ( 1071) hydrogen bonds : angle 4.75111 ( 3117) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 353 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 124 LYS cc_start: 0.8230 (tppp) cc_final: 0.7730 (mtpp) REVERT: A 266 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 464 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7785 (mm) REVERT: B 210 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7503 (mtm180) REVERT: B 294 MET cc_start: 0.7765 (mtt) cc_final: 0.7381 (mtp) REVERT: B 423 ASN cc_start: 0.8441 (t0) cc_final: 0.8001 (t0) REVERT: B 509 MET cc_start: 0.6946 (mmm) cc_final: 0.6723 (mmm) REVERT: C 220 MET cc_start: 0.8243 (tmm) cc_final: 0.7194 (tmm) REVERT: C 266 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 304 TYR cc_start: 0.8654 (m-80) cc_final: 0.8283 (m-80) REVERT: C 393 GLU cc_start: 0.7433 (tt0) cc_final: 0.7176 (tt0) REVERT: D 7 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: D 216 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.6282 (ppt-90) REVERT: D 345 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7837 (mtt90) REVERT: D 381 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7100 (tm130) REVERT: D 401 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: E 111 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8242 (mtp85) REVERT: E 321 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7814 (ttt180) REVERT: E 327 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: E 381 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7726 (tp40) REVERT: E 394 LYS cc_start: 0.7451 (ttpt) cc_final: 0.7231 (tppt) REVERT: E 427 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: F 111 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7318 (mtm-85) REVERT: F 180 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: F 290 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7990 (t0) REVERT: F 362 MET cc_start: 0.8711 (ttt) cc_final: 0.8416 (ttt) REVERT: F 410 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6645 (mtm-85) REVERT: G 26 ASP cc_start: 0.7455 (m-30) cc_final: 0.7239 (m-30) REVERT: G 44 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.7011 (tpt90) REVERT: G 55 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6697 (tm-30) REVERT: G 58 LYS cc_start: 0.7105 (mtpt) cc_final: 0.6270 (tptt) REVERT: G 59 GLU cc_start: 0.6835 (tp30) cc_final: 0.6547 (mm-30) REVERT: G 64 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6535 (tp) REVERT: G 154 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7280 (tt) REVERT: G 185 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: G 200 LYS cc_start: 0.7330 (ttmm) cc_final: 0.7040 (mptt) REVERT: H 1 MET cc_start: 0.6881 (mpt) cc_final: 0.6574 (mpt) REVERT: H 96 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5519 (pttp) outliers start: 181 outliers final: 117 residues processed: 503 average time/residue: 0.1768 time to fit residues: 139.0669 Evaluate side-chains 445 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 309 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 260 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS D 94 ASN D 262 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098909 restraints weight = 41239.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102656 restraints weight = 25438.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103852 restraints weight = 15351.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104576 restraints weight = 11797.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104760 restraints weight = 11600.040| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27154 Z= 0.202 Angle : 0.613 7.548 36793 Z= 0.315 Chirality : 0.046 0.216 4109 Planarity : 0.005 0.082 4818 Dihedral : 9.061 85.493 3991 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.35 % Favored : 90.62 % Rotamer: Outliers : 7.20 % Allowed : 19.54 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 3402 helix: 1.04 (0.15), residues: 1307 sheet: -2.37 (0.22), residues: 506 loop : -2.92 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 416 TYR 0.018 0.001 TYR D 13 PHE 0.016 0.002 PHE B 559 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00491 (27153) covalent geometry : angle 0.61335 (36793) hydrogen bonds : bond 0.05964 ( 1071) hydrogen bonds : angle 4.84455 ( 3117) Misc. bond : bond 0.00179 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 314 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 124 LYS cc_start: 0.8308 (tppp) cc_final: 0.7810 (mtpp) REVERT: A 266 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8651 (mm) REVERT: A 353 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7423 (p90) REVERT: A 464 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7950 (mm) REVERT: B 210 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7967 (mtm110) REVERT: B 294 MET cc_start: 0.8225 (mtt) cc_final: 0.7953 (mtp) REVERT: B 335 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8285 (ttm170) REVERT: B 348 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 423 ASN cc_start: 0.8466 (t0) cc_final: 0.8148 (t0) REVERT: B 489 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 558 GLU cc_start: 0.6989 (tp30) cc_final: 0.6770 (tp30) REVERT: C 116 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7883 (ptpp) REVERT: C 220 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7299 (tmm) REVERT: C 266 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 304 TYR cc_start: 0.8778 (m-80) cc_final: 0.8408 (m-80) REVERT: C 393 GLU cc_start: 0.7520 (tt0) cc_final: 0.7309 (tt0) REVERT: D 7 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: D 216 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.6367 (ppt-90) REVERT: D 268 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6985 (ttt180) REVERT: D 345 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8110 (mtt90) REVERT: D 370 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8096 (mttp) REVERT: D 381 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7331 (tm130) REVERT: E 89 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8011 (mm) REVERT: E 111 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: E 321 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7837 (ttt180) REVERT: E 327 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: E 381 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7743 (tp40) REVERT: E 394 LYS cc_start: 0.7486 (ttpt) cc_final: 0.7122 (tppt) REVERT: E 398 ILE cc_start: 0.6994 (tp) cc_final: 0.6566 (pt) REVERT: E 427 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: F 111 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7337 (mtm-85) REVERT: F 290 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (t0) REVERT: F 362 MET cc_start: 0.8808 (ttt) cc_final: 0.8513 (ttt) REVERT: F 409 ARG cc_start: 0.7312 (ttm110) cc_final: 0.6729 (mtm110) REVERT: F 410 ARG cc_start: 0.7419 (mtt-85) cc_final: 0.6942 (mtm-85) REVERT: G 55 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6854 (tm-30) REVERT: G 58 LYS cc_start: 0.7169 (mtpt) cc_final: 0.6318 (tptt) REVERT: G 64 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6676 (tp) REVERT: G 154 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7580 (tt) REVERT: G 185 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7877 (tp40) REVERT: G 200 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7102 (mptt) REVERT: H 87 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7962 (tm-30) REVERT: H 96 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.5535 (pttp) outliers start: 202 outliers final: 144 residues processed: 477 average time/residue: 0.1809 time to fit residues: 133.8276 Evaluate side-chains 467 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 298 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 300 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** 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 = 0.3417 r_free = 0.3417 target = 0.124748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101611 restraints weight = 40875.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104821 restraints weight = 25392.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106536 restraints weight = 15668.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107955 restraints weight = 11656.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108089 restraints weight = 10852.571| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27154 Z= 0.126 Angle : 0.555 7.748 36793 Z= 0.284 Chirality : 0.044 0.186 4109 Planarity : 0.005 0.077 4818 Dihedral : 8.637 82.404 3982 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 6.35 % Allowed : 20.33 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 3402 helix: 1.30 (0.15), residues: 1295 sheet: -2.13 (0.23), residues: 497 loop : -2.77 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 44 TYR 0.017 0.001 TYR A 513 PHE 0.013 0.001 PHE C 419 TRP 0.011 0.001 TRP C 119 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00291 (27153) covalent geometry : angle 0.55545 (36793) hydrogen bonds : bond 0.04922 ( 1071) hydrogen bonds : angle 4.67354 ( 3117) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 324 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8251 (tppp) cc_final: 0.7732 (mtpp) REVERT: A 266 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (mm) REVERT: B 210 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7972 (mtm180) REVERT: B 262 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7295 (mmm) REVERT: B 294 MET cc_start: 0.8070 (mtt) cc_final: 0.7754 (mtp) REVERT: B 335 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8250 (ttm170) REVERT: B 348 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 423 ASN cc_start: 0.8434 (t0) cc_final: 0.8015 (t0) REVERT: B 570 ILE cc_start: 0.8387 (mt) cc_final: 0.8083 (mt) REVERT: C 116 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7859 (ptpp) REVERT: C 141 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7767 (p90) REVERT: C 220 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: C 266 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8638 (mt) REVERT: C 304 TYR cc_start: 0.8707 (m-80) cc_final: 0.8339 (m-80) REVERT: C 393 GLU cc_start: 0.7505 (tt0) cc_final: 0.7282 (tt0) REVERT: D 7 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6681 (pt0) REVERT: D 216 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.6386 (ppt-90) REVERT: D 268 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6810 (ttt180) REVERT: D 345 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7994 (mtt90) REVERT: D 370 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8050 (mttp) REVERT: D 381 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7167 (tm130) REVERT: D 401 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6511 (mm-30) REVERT: E 89 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7817 (mm) REVERT: E 111 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8238 (mtp85) REVERT: E 321 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7733 (ttt180) REVERT: E 327 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: E 394 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7123 (tppt) REVERT: E 398 ILE cc_start: 0.6945 (tp) cc_final: 0.6539 (pt) REVERT: E 427 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: F 276 GLU cc_start: 0.7624 (tt0) cc_final: 0.7318 (tt0) REVERT: F 290 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8023 (t0) REVERT: F 362 MET cc_start: 0.8734 (ttt) cc_final: 0.8450 (ttt) REVERT: F 410 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6779 (mtm-85) REVERT: G 55 GLN cc_start: 0.7313 (tm-30) cc_final: 0.7032 (tm-30) REVERT: G 58 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6215 (tptt) REVERT: G 64 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6646 (tp) REVERT: G 154 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7385 (tt) REVERT: G 162 ASN cc_start: 0.8030 (m110) cc_final: 0.7795 (m110) REVERT: G 181 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7679 (mm-40) REVERT: G 185 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7775 (tp40) REVERT: G 200 LYS cc_start: 0.7363 (ttmm) cc_final: 0.7133 (mptt) REVERT: H 19 GLU cc_start: 0.7132 (pt0) cc_final: 0.6667 (pm20) REVERT: H 60 GLU cc_start: 0.5013 (tt0) cc_final: 0.4799 (pp20) REVERT: H 87 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7906 (tm-30) REVERT: H 96 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5521 (pttp) outliers start: 178 outliers final: 127 residues processed: 466 average time/residue: 0.1776 time to fit residues: 129.2384 Evaluate side-chains 449 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 298 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 574 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 298 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098846 restraints weight = 41136.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102412 restraints weight = 25467.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103482 restraints weight = 15674.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104668 restraints weight = 12484.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104755 restraints weight = 11713.044| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27154 Z= 0.209 Angle : 0.610 7.616 36793 Z= 0.313 Chirality : 0.046 0.184 4109 Planarity : 0.005 0.082 4818 Dihedral : 8.577 78.730 3963 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.82 % Favored : 90.15 % Rotamer: Outliers : 7.03 % Allowed : 20.04 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 3402 helix: 1.15 (0.15), residues: 1302 sheet: -2.16 (0.23), residues: 503 loop : -2.79 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 416 TYR 0.019 0.001 TYR A 513 PHE 0.015 0.002 PHE B 559 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00512 (27153) covalent geometry : angle 0.61016 (36793) hydrogen bonds : bond 0.05941 ( 1071) hydrogen bonds : angle 4.79901 ( 3117) Misc. bond : bond 0.00173 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 306 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 100 " (corrupted residue). Skipping it. REVERT: A 95 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (tmt-80) REVERT: A 124 LYS cc_start: 0.8305 (tppp) cc_final: 0.7831 (mtpp) REVERT: A 266 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8608 (mm) REVERT: A 353 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7450 (p90) REVERT: B 210 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8286 (mtm180) REVERT: B 294 MET cc_start: 0.8288 (mtt) cc_final: 0.8013 (mtp) REVERT: B 335 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8259 (ttm170) REVERT: B 348 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 423 ASN cc_start: 0.8477 (t0) cc_final: 0.8162 (t0) REVERT: B 570 ILE cc_start: 0.8427 (mt) cc_final: 0.8123 (mt) REVERT: C 116 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7895 (ptpp) REVERT: C 220 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7827 (tmm) REVERT: C 266 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 304 TYR cc_start: 0.8789 (m-80) cc_final: 0.8415 (m-80) REVERT: C 393 GLU cc_start: 0.7574 (tt0) cc_final: 0.7343 (tt0) REVERT: D 7 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6604 (pt0) REVERT: D 216 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.6412 (ppt-90) REVERT: D 268 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6975 (ttt180) REVERT: D 270 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8711 (mt) REVERT: D 345 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8099 (mtt90) REVERT: D 370 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8086 (mttp) REVERT: D 381 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7304 (tm130) REVERT: D 401 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6505 (mm-30) REVERT: E 111 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8183 (mtp85) REVERT: E 321 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7764 (ttt180) REVERT: E 327 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: E 394 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7096 (tppt) REVERT: E 398 ILE cc_start: 0.7027 (tp) cc_final: 0.6579 (pt) REVERT: E 401 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7383 (tm-30) REVERT: E 427 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: F 111 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7288 (mtm-85) REVERT: F 276 GLU cc_start: 0.7658 (tt0) cc_final: 0.7442 (tt0) REVERT: F 290 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8209 (t0) REVERT: F 331 TYR cc_start: 0.8291 (m-80) cc_final: 0.7756 (m-80) REVERT: F 362 MET cc_start: 0.8813 (ttt) cc_final: 0.8514 (ttt) REVERT: F 406 GLU cc_start: 0.6469 (tm-30) cc_final: 0.6181 (tm-30) REVERT: F 410 ARG cc_start: 0.7321 (mtt-85) cc_final: 0.6771 (mtm-85) REVERT: G 55 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7023 (tm-30) REVERT: G 58 LYS cc_start: 0.7160 (mtpt) cc_final: 0.6341 (tptt) REVERT: G 64 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6688 (tp) REVERT: G 86 LEU cc_start: 0.2851 (OUTLIER) cc_final: 0.2637 (pp) REVERT: G 154 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7549 (tt) REVERT: G 185 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7840 (tp40) REVERT: G 200 LYS cc_start: 0.7421 (ttmm) cc_final: 0.7186 (mptt) REVERT: H 19 GLU cc_start: 0.7191 (pt0) cc_final: 0.6762 (pm20) REVERT: H 60 GLU cc_start: 0.5179 (tt0) cc_final: 0.4902 (pp20) REVERT: H 87 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7818 (tm-30) REVERT: H 96 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5520 (pttp) outliers start: 197 outliers final: 145 residues processed: 464 average time/residue: 0.1768 time to fit residues: 128.6649 Evaluate side-chains 467 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 296 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 229 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 233 optimal weight: 0.3980 chunk 293 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** 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 = 0.3429 r_free = 0.3429 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102510 restraints weight = 40910.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105943 restraints weight = 25164.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.107052 restraints weight = 15773.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108480 restraints weight = 12463.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108542 restraints weight = 11303.892| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27154 Z= 0.121 Angle : 0.556 7.613 36793 Z= 0.284 Chirality : 0.044 0.167 4109 Planarity : 0.005 0.076 4818 Dihedral : 8.314 75.557 3963 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 6.06 % Allowed : 21.01 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3402 helix: 1.42 (0.15), residues: 1289 sheet: -1.88 (0.24), residues: 480 loop : -2.63 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 416 TYR 0.014 0.001 TYR A 513 PHE 0.013 0.001 PHE C 419 TRP 0.010 0.001 TRP C 119 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00277 (27153) covalent geometry : angle 0.55625 (36793) hydrogen bonds : bond 0.04824 ( 1071) hydrogen bonds : angle 4.62992 ( 3117) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 322 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8188 (tmt-80) REVERT: A 124 LYS cc_start: 0.8258 (tppp) cc_final: 0.7744 (mtpp) REVERT: A 266 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8375 (mm) REVERT: B 210 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8252 (mtm180) REVERT: B 335 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8245 (ttm170) REVERT: B 348 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 423 ASN cc_start: 0.8401 (t0) cc_final: 0.8014 (t0) REVERT: B 570 ILE cc_start: 0.8394 (mt) cc_final: 0.8100 (mt) REVERT: C 116 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7888 (ptpp) REVERT: C 141 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7857 (p90) REVERT: C 220 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7824 (tmm) REVERT: C 266 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8617 (mt) REVERT: C 304 TYR cc_start: 0.8711 (m-80) cc_final: 0.8355 (m-80) REVERT: C 393 GLU cc_start: 0.7521 (tt0) cc_final: 0.7302 (tt0) REVERT: D 7 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: D 216 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.6417 (ppt-90) REVERT: D 268 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.6787 (ttt180) REVERT: D 345 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7985 (mtt90) REVERT: D 370 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (mttp) REVERT: D 381 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7166 (tm130) REVERT: D 401 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: E 111 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8203 (mtp85) REVERT: E 290 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7873 (t70) REVERT: E 321 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7669 (ttt180) REVERT: E 327 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: E 358 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8199 (pt) REVERT: E 381 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7621 (tp40) REVERT: E 394 LYS cc_start: 0.7319 (ttpt) cc_final: 0.6902 (tppt) REVERT: E 398 ILE cc_start: 0.6925 (tp) cc_final: 0.6465 (pt) REVERT: E 427 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: F 91 ARG cc_start: 0.8483 (mmm160) cc_final: 0.7926 (mmm-85) REVERT: F 111 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7244 (mtm-85) REVERT: F 180 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: F 290 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8018 (t0) REVERT: F 362 MET cc_start: 0.8737 (ttt) cc_final: 0.8455 (ttt) REVERT: F 410 ARG cc_start: 0.7173 (mtt-85) cc_final: 0.6692 (mtm-85) REVERT: F 442 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8160 (mt) REVERT: G 55 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7055 (tm-30) REVERT: G 58 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6210 (tptt) REVERT: G 64 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6661 (tp) REVERT: G 185 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7777 (tp40) REVERT: G 200 LYS cc_start: 0.7321 (ttmm) cc_final: 0.7010 (mptt) REVERT: H 19 GLU cc_start: 0.7161 (pt0) cc_final: 0.6763 (pm20) REVERT: H 60 GLU cc_start: 0.5100 (tt0) cc_final: 0.4816 (pp20) REVERT: H 87 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7878 (tm-30) REVERT: H 96 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5455 (pttp) outliers start: 170 outliers final: 125 residues processed: 458 average time/residue: 0.1748 time to fit residues: 125.2884 Evaluate side-chains 457 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 305 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 286 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 287 optimal weight: 0.9990 chunk 329 optimal weight: 0.7980 chunk 201 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.104414 restraints weight = 40756.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107875 restraints weight = 25354.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109094 restraints weight = 15505.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110556 restraints weight = 12232.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110620 restraints weight = 11106.465| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27154 Z= 0.108 Angle : 0.540 7.005 36793 Z= 0.275 Chirality : 0.043 0.179 4109 Planarity : 0.004 0.073 4818 Dihedral : 7.880 75.219 3948 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 5.10 % Allowed : 22.11 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 3402 helix: 1.57 (0.15), residues: 1293 sheet: -1.71 (0.24), residues: 497 loop : -2.50 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 416 TYR 0.013 0.001 TYR A 513 PHE 0.012 0.001 PHE C 419 TRP 0.009 0.001 TRP C 119 HIS 0.014 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00239 (27153) covalent geometry : angle 0.53962 (36793) hydrogen bonds : bond 0.04292 ( 1071) hydrogen bonds : angle 4.52944 ( 3117) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 325 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (tmt-80) REVERT: A 124 LYS cc_start: 0.8210 (tppp) cc_final: 0.7706 (mtpp) REVERT: A 266 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8367 (mm) REVERT: B 210 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8226 (mtm180) REVERT: B 294 MET cc_start: 0.7542 (mtt) cc_final: 0.7222 (mtp) REVERT: B 335 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8228 (ttm170) REVERT: B 348 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7817 (mm-30) REVERT: B 423 ASN cc_start: 0.8409 (t0) cc_final: 0.8068 (t0) REVERT: B 570 ILE cc_start: 0.8360 (mt) cc_final: 0.8064 (mt) REVERT: C 116 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: C 141 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (p90) REVERT: C 220 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: C 266 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8605 (mt) REVERT: C 304 TYR cc_start: 0.8692 (m-80) cc_final: 0.8322 (m-80) REVERT: C 393 GLU cc_start: 0.7494 (tt0) cc_final: 0.7265 (tt0) REVERT: D 7 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: D 216 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.6368 (ppt-90) REVERT: D 268 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.6833 (ttt180) REVERT: D 345 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7898 (mtt90) REVERT: D 370 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7975 (mttp) REVERT: D 381 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7158 (tm130) REVERT: D 401 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: E 106 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7573 (tp) REVERT: E 290 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (t70) REVERT: E 321 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7656 (ttt180) REVERT: E 327 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: E 358 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8139 (pt) REVERT: E 381 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7623 (tp40) REVERT: E 394 LYS cc_start: 0.7321 (ttpt) cc_final: 0.6907 (tppt) REVERT: E 398 ILE cc_start: 0.6871 (tp) cc_final: 0.6450 (pt) REVERT: E 427 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: F 91 ARG cc_start: 0.8412 (mmm160) cc_final: 0.7880 (mmm-85) REVERT: F 111 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7150 (mtm-85) REVERT: F 180 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: F 290 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7986 (t0) REVERT: F 362 MET cc_start: 0.8722 (ttt) cc_final: 0.8414 (ttt) REVERT: F 410 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6684 (mtm-85) REVERT: G 64 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6720 (tp) REVERT: G 154 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7443 (tt) REVERT: G 185 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7716 (tp40) REVERT: G 200 LYS cc_start: 0.7250 (ttmm) cc_final: 0.6982 (mptt) REVERT: H 19 GLU cc_start: 0.7090 (pt0) cc_final: 0.6724 (pm20) REVERT: H 77 LEU cc_start: 0.2636 (OUTLIER) cc_final: 0.2425 (tp) REVERT: H 87 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7882 (tm-30) outliers start: 143 outliers final: 100 residues processed: 444 average time/residue: 0.1792 time to fit residues: 123.0061 Evaluate side-chains 434 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 307 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 129 optimal weight: 0.0060 chunk 85 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 306 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 334 optimal weight: 5.9990 overall best weight: 0.6208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 HIS ** 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 = 0.3454 r_free = 0.3454 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104424 restraints weight = 40601.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108052 restraints weight = 25081.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109616 restraints weight = 15163.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109989 restraints weight = 11634.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110285 restraints weight = 11307.407| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27154 Z= 0.117 Angle : 0.557 9.702 36793 Z= 0.284 Chirality : 0.044 0.208 4109 Planarity : 0.004 0.074 4818 Dihedral : 7.386 75.301 3920 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 4.64 % Allowed : 22.75 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3402 helix: 1.57 (0.15), residues: 1301 sheet: -1.60 (0.24), residues: 497 loop : -2.45 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 416 TYR 0.014 0.001 TYR A 513 PHE 0.018 0.001 PHE B 574 TRP 0.009 0.001 TRP C 119 HIS 0.007 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00266 (27153) covalent geometry : angle 0.55712 (36793) hydrogen bonds : bond 0.04370 ( 1071) hydrogen bonds : angle 4.54398 ( 3117) Misc. bond : bond 0.00116 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 312 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8187 (tmt-80) REVERT: A 124 LYS cc_start: 0.8134 (tppp) cc_final: 0.7612 (mtpp) REVERT: A 266 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 294 MET cc_start: 0.7559 (mtt) cc_final: 0.7251 (mtp) REVERT: B 335 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8211 (ttm170) REVERT: B 348 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 423 ASN cc_start: 0.8401 (t0) cc_final: 0.8077 (t0) REVERT: B 570 ILE cc_start: 0.8351 (mt) cc_final: 0.8051 (mt) REVERT: C 116 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7883 (ptpp) REVERT: C 141 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7885 (p90) REVERT: C 220 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7891 (tmm) REVERT: C 266 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 393 GLU cc_start: 0.7452 (tt0) cc_final: 0.7240 (tt0) REVERT: D 7 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: D 216 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.6394 (ppt-90) REVERT: D 268 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6838 (ttt180) REVERT: D 381 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7198 (tm130) REVERT: D 401 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: E 106 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7497 (tp) REVERT: E 290 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7825 (t70) REVERT: E 321 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7744 (ttt180) REVERT: E 327 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: E 394 LYS cc_start: 0.7327 (ttpt) cc_final: 0.6897 (tppt) REVERT: E 398 ILE cc_start: 0.6740 (tp) cc_final: 0.6412 (pt) REVERT: E 427 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: F 91 ARG cc_start: 0.8401 (mmm160) cc_final: 0.7876 (mmm-85) REVERT: F 111 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7126 (mtm-85) REVERT: F 180 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: F 225 ASP cc_start: 0.7559 (t70) cc_final: 0.7239 (t70) REVERT: F 276 GLU cc_start: 0.7596 (tt0) cc_final: 0.7041 (tt0) REVERT: F 410 ARG cc_start: 0.7146 (mtt-85) cc_final: 0.6727 (mtm-85) REVERT: G 19 ARG cc_start: 0.7081 (mpt180) cc_final: 0.6825 (mpt180) REVERT: G 44 ARG cc_start: 0.7543 (tpt90) cc_final: 0.7022 (tpp-160) REVERT: G 64 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6658 (tp) REVERT: G 185 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7730 (tp40) REVERT: G 200 LYS cc_start: 0.7264 (ttmm) cc_final: 0.6974 (mptt) REVERT: H 68 LEU cc_start: 0.6982 (mt) cc_final: 0.6483 (mm) outliers start: 130 outliers final: 100 residues processed: 417 average time/residue: 0.1835 time to fit residues: 118.7606 Evaluate side-chains 424 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 304 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 574 PHE Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 320 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 315 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain G residue 8 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 96 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102618 restraints weight = 40776.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105926 restraints weight = 25637.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107108 restraints weight = 15949.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108590 restraints weight = 12581.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108652 restraints weight = 11346.218| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27154 Z= 0.135 Angle : 0.564 7.251 36793 Z= 0.288 Chirality : 0.044 0.195 4109 Planarity : 0.005 0.074 4818 Dihedral : 7.323 74.309 3913 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.73 % Favored : 92.24 % Rotamer: Outliers : 4.71 % Allowed : 22.68 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3402 helix: 1.58 (0.15), residues: 1293 sheet: -1.61 (0.24), residues: 500 loop : -2.43 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 416 TYR 0.016 0.001 TYR A 513 PHE 0.014 0.001 PHE B 574 TRP 0.009 0.001 TRP C 119 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00320 (27153) covalent geometry : angle 0.56448 (36793) hydrogen bonds : bond 0.04745 ( 1071) hydrogen bonds : angle 4.57918 ( 3117) Misc. bond : bond 0.00128 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4129.11 seconds wall clock time: 71 minutes 52.34 seconds (4312.34 seconds total)