Starting phenix.real_space_refine on Fri Mar 6 02:33:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.map" model { file = "/net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vog_21263/03_2026/6vog_21263.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 14 5.49 5 S 98 5.16 5 C 17048 2.51 5 N 4689 2.21 5 O 5288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 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: 27137 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3796 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3832 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3829 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3589 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3600 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3610 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1360 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "e" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 926 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.21 Number of scatterers: 27137 At special positions: 0 Unit cell: (131.04, 151.84, 133.12, 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 98 16.00 P 14 15.00 O 5288 8.00 N 4689 7.00 C 17048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6546 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 26 sheets defined 47.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.418A pdb=" N MET A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.649A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 221 removed outlier: 4.215A pdb=" N GLU A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.606A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 373 through 395 removed outlier: 4.422A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 5.507A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.763A pdb=" N SER A 448 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.868A pdb=" N ARG A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 3.983A pdb=" N GLN A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.529A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.978A pdb=" N THR B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.958A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.295A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 371 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.639A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.014A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 502 removed outlier: 3.788A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.702A pdb=" N ASP C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 221 removed outlier: 3.633A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.668A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.649A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.696A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 330 through 338 removed outlier: 4.150A pdb=" N ILE C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 421 Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.756A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 5.250A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.603A pdb=" N GLU D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.766A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 402 Processing helix chain 'D' and resid 404 through 409 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 3.939A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.509A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 330 through 333 removed outlier: 4.111A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 383 through 409 removed outlier: 4.831A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 432 removed outlier: 4.761A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 removed outlier: 3.660A pdb=" N SER E 463 " --> pdb=" O GLN E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 496 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 153 through 160 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 242 through 263 removed outlier: 4.504A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.830A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.867A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.742A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 406 removed outlier: 3.904A pdb=" N THR F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 450 through 464 removed outlier: 4.223A pdb=" N PHE F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 removed outlier: 3.965A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 493 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 3.528A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 173 removed outlier: 4.208A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 237 through 248 removed outlier: 4.279A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 removed outlier: 3.505A pdb=" N ALA g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 132 through 152 removed outlier: 4.681A pdb=" N LEU g 138 " --> pdb=" O ASN g 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 Processing helix chain 'g' and resid 187 through 204 removed outlier: 4.342A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP g 197 " --> pdb=" O ALA g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 291 through 362 Proline residue: g 297 - end of helix removed outlier: 4.191A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 87 removed outlier: 3.994A pdb=" N ASP e 86 " --> pdb=" O ARG e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 3.626A pdb=" N LEU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 131 removed outlier: 3.857A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.564A pdb=" N LEU A 33 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 63 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 26 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.536A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.571A pdb=" N LEU A 258 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.332A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 35 " --> pdb=" O LEU E 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA5, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.332A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 68 current: chain 'B' and resid 53 through 55 removed outlier: 5.722A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.165A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.410A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 257 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.546A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 169 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 231 through 232 removed outlier: 3.860A pdb=" N VAL C 27 " --> pdb=" O LEU d 232 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 63 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU C 67 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.685A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.529A pdb=" N VAL C 160 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 193 through 198 removed outlier: 5.882A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 257 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU C 317 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 259 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE C 319 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR C 261 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLU C 321 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 168 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 21 through 27 removed outlier: 4.942A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 30 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 50 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 21 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.883A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 271 removed outlier: 5.671A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 200 through 204 removed outlier: 6.159A pdb=" N GLY D 201 " --> pdb=" O GLY D 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC1, first strand: chain 'E' and resid 234 through 238 removed outlier: 3.947A pdb=" N GLY E 200 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR E 328 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'F' and resid 235 through 238 removed outlier: 7.465A pdb=" N VAL F 235 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE F 199 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY F 237 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY F 201 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 273 " --> pdb=" O GLY F 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 178 through 179 removed outlier: 6.166A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'g' and resid 178 through 180 removed outlier: 3.771A pdb=" N ARG g 178 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR g 214 " --> pdb=" O VAL g 226 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 253 through 258 removed outlier: 3.747A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP g 269 " --> pdb=" O LEU g 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 283 through 284 removed outlier: 6.604A pdb=" N GLU g 283 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ALA e 43 " --> pdb=" O GLU g 283 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR e 42 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 24 through 26 1290 hydrogen bonds defined for protein. 3714 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: 4.94 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8222 1.33 - 1.45: 3776 1.45 - 1.57: 15307 1.57 - 1.69: 23 1.69 - 1.81: 185 Bond restraints: 27513 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 27508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 37019 4.29 - 8.58: 279 8.58 - 12.86: 20 12.86 - 17.15: 2 17.15 - 21.44: 7 Bond angle restraints: 37327 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 118.43 21.44 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.32 20.55 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.14 19.69 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 120.88 18.99 1.00e+00 1.00e+00 3.61e+02 ... (remaining 37322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 15609 23.61 - 47.22: 1133 47.22 - 70.84: 125 70.84 - 94.45: 48 94.45 - 118.06: 3 Dihedral angle restraints: 16918 sinusoidal: 6718 harmonic: 10200 Sorted by residual: dihedral pdb=" CA TYR D 362 " pdb=" C TYR D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual 180.00 120.03 59.97 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.78 -52.22 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 16915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3958 0.090 - 0.181: 438 0.181 - 0.271: 24 0.271 - 0.361: 4 0.361 - 0.452: 1 Chirality restraints: 4425 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 4422 not shown) Planarity restraints: 4851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 362 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 363 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 363 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 363 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 338 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO F 339 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ALA D 295 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA D 295 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL D 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 4848 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6283 2.77 - 3.31: 29182 3.31 - 3.84: 50500 3.84 - 4.37: 57908 4.37 - 4.90: 93750 Nonbonded interactions: 237623 Sorted by model distance: nonbonded pdb=" OH TYR B 330 " pdb=" OE2 GLU D 284 " model vdw 2.242 3.040 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.243 3.040 nonbonded pdb=" O GLY F 450 " pdb=" OG1 THR F 454 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 228 " pdb=" OD1 ASP A 230 " model vdw 2.253 3.040 nonbonded pdb=" O ILE A 475 " pdb=" OG1 THR A 479 " model vdw 2.258 3.040 ... (remaining 237618 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 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 322 or (resid 323 thro \ ugh 324 and (name N or name CA or name C or name O or name CB )) or resid 325 th \ rough 398 or (resid 399 through 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 601)) selection = (chain 'B' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 393 or (resid 394 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 through 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 503 or resid 601)) selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 23 or (resid 24 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 322 or (resid 323 through 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 393 or \ (resid 394 through 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 471 or (resid 472 and (name N or name CA or \ name C or name O or name CB )) or resid 473 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 58 or (resid 59 and ( \ name N or name CA or name C or name O or name CB )) or resid 60 through 115 or ( \ resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ through 118 or (resid 119 and (name N or name CA or name C or name O or name CB \ )) or resid 120 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 416 or ( \ resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ through 494)) selection = (chain 'E' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 260 or (resid 261 and \ (name N or name CA or name C or name O or name CB )) or resid 262 through 331 o \ r (resid 332 through 333 and (name N or name CA or name C or name O or name CB ) \ ) or resid 334 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 446 or (resid 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 464 or (r \ esid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 t \ hrough 494)) selection = (chain 'F' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 78 or \ (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 t \ hrough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ) \ ) or resid 117 through 118 or (resid 119 and (name N or name CA or name C or nam \ e O or name CB )) or resid 120 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 through 331 or (r \ esid 332 through 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 464 or (resid 465 and (na \ me N or name CA or name C or name O or name CB )) or resid 466 through 494)) } 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.007 0.081 27514 Z= 0.352 Angle : 1.079 21.440 37329 Z= 0.658 Chirality : 0.056 0.452 4425 Planarity : 0.007 0.072 4851 Dihedral : 16.400 118.062 10369 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 0.49 % Allowed : 13.12 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.15 % 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: -3.94 (0.12), residues: 3544 helix: -2.16 (0.10), residues: 1482 sheet: -3.57 (0.20), residues: 441 loop : -2.68 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 107 TYR 0.024 0.003 TYR A 271 PHE 0.037 0.003 PHE F 343 TRP 0.020 0.003 TRP e 15 HIS 0.009 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00662 (27513) covalent geometry : angle 1.07846 (37327) SS BOND : bond 0.00477 ( 1) SS BOND : angle 1.69738 ( 2) hydrogen bonds : bond 0.14607 ( 1280) hydrogen bonds : angle 7.38149 ( 3714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 950 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7037 (tp30) cc_final: 0.6736 (tp30) REVERT: A 76 LEU cc_start: 0.9453 (mt) cc_final: 0.9224 (mt) REVERT: A 169 ILE cc_start: 0.8396 (tp) cc_final: 0.8183 (tp) REVERT: A 219 MET cc_start: 0.8268 (ppp) cc_final: 0.8001 (ppp) REVERT: A 230 ASP cc_start: 0.7896 (p0) cc_final: 0.7527 (p0) REVERT: A 251 MET cc_start: 0.8095 (tmm) cc_final: 0.7552 (ttp) REVERT: A 266 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7569 (mmmm) REVERT: A 278 LEU cc_start: 0.7752 (mt) cc_final: 0.7481 (mt) REVERT: A 287 TYR cc_start: 0.7333 (m-80) cc_final: 0.7004 (m-80) REVERT: A 292 PHE cc_start: 0.8164 (t80) cc_final: 0.7617 (t80) REVERT: A 300 GLU cc_start: 0.8491 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 309 LEU cc_start: 0.9223 (mm) cc_final: 0.8992 (tt) REVERT: A 314 MET cc_start: 0.7629 (ttm) cc_final: 0.7293 (ttp) REVERT: A 333 THR cc_start: 0.9105 (t) cc_final: 0.8714 (t) REVERT: A 349 LEU cc_start: 0.9243 (mt) cc_final: 0.9024 (mt) REVERT: A 376 MET cc_start: 0.7723 (tpp) cc_final: 0.7417 (tpp) REVERT: A 436 MET cc_start: 0.9145 (ppp) cc_final: 0.8670 (ppp) REVERT: A 464 TYR cc_start: 0.7360 (t80) cc_final: 0.7144 (t80) REVERT: B 15 GLU cc_start: 0.9137 (tt0) cc_final: 0.8546 (mm-30) REVERT: B 147 LEU cc_start: 0.8825 (tt) cc_final: 0.8554 (tt) REVERT: B 194 CYS cc_start: 0.8988 (m) cc_final: 0.8560 (m) REVERT: B 278 LEU cc_start: 0.9333 (mm) cc_final: 0.9105 (mm) REVERT: B 293 TYR cc_start: 0.7062 (t80) cc_final: 0.6038 (t80) REVERT: B 360 VAL cc_start: 0.8372 (m) cc_final: 0.8156 (t) REVERT: B 386 GLU cc_start: 0.7975 (tp30) cc_final: 0.7273 (tm-30) REVERT: B 449 LEU cc_start: 0.7171 (mm) cc_final: 0.6669 (mm) REVERT: B 453 GLN cc_start: 0.9216 (mm110) cc_final: 0.8987 (mp10) REVERT: B 480 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8411 (mmtt) REVERT: C 14 ARG cc_start: 0.5918 (mmt90) cc_final: 0.5505 (mpt180) REVERT: C 49 MET cc_start: 0.7734 (tpt) cc_final: 0.6206 (tpt) REVERT: C 55 GLU cc_start: 0.8337 (tp30) cc_final: 0.8111 (tp30) REVERT: C 77 MET cc_start: 0.7670 (ppp) cc_final: 0.7435 (ppp) REVERT: C 108 VAL cc_start: 0.9053 (t) cc_final: 0.8658 (t) REVERT: C 194 CYS cc_start: 0.8645 (m) cc_final: 0.7560 (m) REVERT: C 219 MET cc_start: 0.8011 (ptm) cc_final: 0.7475 (ptm) REVERT: C 228 THR cc_start: 0.8442 (p) cc_final: 0.7960 (t) REVERT: C 251 MET cc_start: 0.8047 (ttp) cc_final: 0.6997 (ttp) REVERT: C 258 LEU cc_start: 0.9236 (tt) cc_final: 0.8991 (tt) REVERT: C 271 TYR cc_start: 0.8235 (t80) cc_final: 0.7957 (t80) REVERT: C 273 GLN cc_start: 0.8343 (tt0) cc_final: 0.7775 (tt0) REVERT: C 345 LEU cc_start: 0.7801 (mm) cc_final: 0.7004 (mp) REVERT: C 392 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 433 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6703 (tp30) REVERT: C 434 GLN cc_start: 0.9076 (mt0) cc_final: 0.8529 (mt0) REVERT: C 436 MET cc_start: 0.8116 (mtt) cc_final: 0.7806 (mtt) REVERT: C 449 LEU cc_start: 0.8582 (mt) cc_final: 0.8150 (mt) REVERT: C 462 ARG cc_start: 0.8843 (ptm-80) cc_final: 0.8355 (ptm-80) REVERT: C 489 LEU cc_start: 0.9122 (mt) cc_final: 0.8365 (mt) REVERT: D 64 GLU cc_start: 0.7760 (mp0) cc_final: 0.7415 (mp0) REVERT: D 65 VAL cc_start: 0.7968 (t) cc_final: 0.7763 (t) REVERT: D 89 MET cc_start: 0.8012 (ttm) cc_final: 0.7669 (mtt) REVERT: D 182 ILE cc_start: 0.8629 (mt) cc_final: 0.8370 (mm) REVERT: D 199 PHE cc_start: 0.8957 (t80) cc_final: 0.8500 (t80) REVERT: D 204 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 212 LEU cc_start: 0.9334 (tp) cc_final: 0.9077 (tt) REVERT: D 247 MET cc_start: 0.8862 (ttp) cc_final: 0.8326 (ttt) REVERT: D 335 THR cc_start: 0.8966 (t) cc_final: 0.8598 (m) REVERT: D 345 HIS cc_start: 0.7095 (t70) cc_final: 0.6093 (t70) REVERT: D 366 ASP cc_start: 0.8285 (t70) cc_final: 0.7973 (t0) REVERT: D 401 LEU cc_start: 0.8591 (mm) cc_final: 0.8343 (tt) REVERT: D 418 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8570 (ttp80) REVERT: D 469 LEU cc_start: 0.8677 (mt) cc_final: 0.8470 (mt) REVERT: E 79 MET cc_start: 0.8198 (mpp) cc_final: 0.6688 (mpp) REVERT: E 102 VAL cc_start: 0.8652 (m) cc_final: 0.7999 (p) REVERT: E 251 LEU cc_start: 0.8052 (tp) cc_final: 0.7485 (tp) REVERT: E 264 ASN cc_start: 0.8133 (m110) cc_final: 0.7847 (t0) REVERT: E 328 TYR cc_start: 0.8422 (t80) cc_final: 0.8133 (t80) REVERT: E 386 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7954 (mm-30) REVERT: E 393 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7600 (tp30) REVERT: E 439 GLU cc_start: 0.8042 (pp20) cc_final: 0.7224 (pm20) REVERT: E 455 ILE cc_start: 0.9167 (pt) cc_final: 0.8801 (mm) REVERT: E 456 ARG cc_start: 0.8428 (tmt-80) cc_final: 0.8081 (tmm160) REVERT: F 168 ILE cc_start: 0.7662 (mm) cc_final: 0.7332 (mt) REVERT: F 213 TYR cc_start: 0.8482 (t80) cc_final: 0.8222 (t80) REVERT: F 214 MET cc_start: 0.8213 (mmp) cc_final: 0.7886 (tmm) REVERT: F 239 MET cc_start: 0.7905 (ttm) cc_final: 0.7424 (ttm) REVERT: F 306 MET cc_start: 0.8408 (tpp) cc_final: 0.7880 (tpt) REVERT: F 475 TYR cc_start: 0.7626 (t80) cc_final: 0.7392 (t80) REVERT: F 481 ASP cc_start: 0.8361 (m-30) cc_final: 0.8126 (m-30) REVERT: F 482 GLU cc_start: 0.8653 (tp30) cc_final: 0.8334 (tp30) REVERT: F 486 LYS cc_start: 0.8901 (tttp) cc_final: 0.8507 (tppp) REVERT: d 84 ASP cc_start: 0.8816 (t0) cc_final: 0.8550 (t0) REVERT: d 98 ASP cc_start: 0.8844 (t0) cc_final: 0.8543 (t0) REVERT: d 104 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8327 (mmm-85) REVERT: d 112 TYR cc_start: 0.8711 (t80) cc_final: 0.8412 (t80) REVERT: d 114 PHE cc_start: 0.8967 (t80) cc_final: 0.8234 (t80) REVERT: d 125 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7709 (mtpp) REVERT: d 164 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6178 (tp30) REVERT: d 167 ASP cc_start: 0.8860 (t70) cc_final: 0.8588 (p0) REVERT: d 193 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8514 (tt0) REVERT: d 235 MET cc_start: 0.7276 (ttp) cc_final: 0.7032 (ttp) REVERT: g 64 MET cc_start: 0.7921 (tpp) cc_final: 0.7420 (tpp) REVERT: g 96 MET cc_start: 0.8356 (mmp) cc_final: 0.7906 (mmm) REVERT: g 189 LYS cc_start: 0.8839 (mttp) cc_final: 0.8384 (mmmt) REVERT: g 287 ASP cc_start: 0.8787 (t70) cc_final: 0.8536 (m-30) REVERT: g 310 GLU cc_start: 0.8300 (tt0) cc_final: 0.7565 (tp30) REVERT: e 11 ASN cc_start: 0.8219 (p0) cc_final: 0.8014 (p0) REVERT: e 53 LEU cc_start: 0.6818 (tp) cc_final: 0.6614 (mt) REVERT: e 54 ASN cc_start: 0.8494 (m110) cc_final: 0.8211 (m-40) REVERT: e 124 THR cc_start: 0.8330 (m) cc_final: 0.7821 (m) REVERT: e 127 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7704 (mp0) outliers start: 14 outliers final: 5 residues processed: 958 average time/residue: 0.1832 time to fit residues: 273.7195 Evaluate side-chains 602 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 597 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 66 ASN A 173 GLN A 214 GLN A 342 GLN A 389 GLN A 497 GLN B 186 ASN B 256 HIS B 468 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 201 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN C 473 GLN C 497 GLN D 45 ASN D 120 ASN D 433 GLN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN F 72 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN g 58 GLN g 286 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 54 ASN e 56 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078634 restraints weight = 85039.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080969 restraints weight = 47407.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082494 restraints weight = 29869.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083586 restraints weight = 20775.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084248 restraints weight = 15651.518| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27514 Z= 0.152 Angle : 0.725 11.599 37329 Z= 0.373 Chirality : 0.046 0.253 4425 Planarity : 0.006 0.066 4851 Dihedral : 8.533 117.785 4002 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.94 % Favored : 93.03 % Rotamer: Outliers : 0.14 % Allowed : 5.79 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -2.77 (0.13), residues: 3544 helix: -0.88 (0.12), residues: 1490 sheet: -3.38 (0.19), residues: 487 loop : -2.19 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 22 TYR 0.028 0.002 TYR A 221 PHE 0.033 0.002 PHE F 343 TRP 0.011 0.002 TRP e 15 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00330 (27513) covalent geometry : angle 0.72510 (37327) SS BOND : bond 0.00037 ( 1) SS BOND : angle 1.02797 ( 2) hydrogen bonds : bond 0.04545 ( 1280) hydrogen bonds : angle 5.93137 ( 3714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 814 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8927 (pt) cc_final: 0.8167 (pt) REVERT: A 199 ILE cc_start: 0.9089 (mt) cc_final: 0.8862 (mt) REVERT: A 230 ASP cc_start: 0.7438 (p0) cc_final: 0.6829 (p0) REVERT: A 251 MET cc_start: 0.8063 (tmm) cc_final: 0.7524 (ttp) REVERT: A 263 ASP cc_start: 0.7738 (t0) cc_final: 0.7491 (t0) REVERT: A 287 TYR cc_start: 0.7574 (m-80) cc_final: 0.7140 (m-80) REVERT: A 292 PHE cc_start: 0.8071 (t80) cc_final: 0.7669 (t80) REVERT: A 300 GLU cc_start: 0.8828 (tt0) cc_final: 0.8213 (mt-10) REVERT: A 348 ASP cc_start: 0.8427 (p0) cc_final: 0.8122 (p0) REVERT: A 436 MET cc_start: 0.8828 (ppp) cc_final: 0.8391 (ppp) REVERT: A 498 MET cc_start: 0.7900 (mmm) cc_final: 0.7336 (tpt) REVERT: B 14 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8111 (ttp-110) REVERT: B 157 MET cc_start: 0.7795 (mmm) cc_final: 0.7172 (tpp) REVERT: B 171 ASP cc_start: 0.7086 (t0) cc_final: 0.6695 (m-30) REVERT: B 194 CYS cc_start: 0.8198 (m) cc_final: 0.7886 (m) REVERT: B 274 MET cc_start: 0.8838 (ptm) cc_final: 0.8116 (tmm) REVERT: B 293 TYR cc_start: 0.7251 (t80) cc_final: 0.6114 (t80) REVERT: B 386 GLU cc_start: 0.7191 (tp30) cc_final: 0.6919 (tm-30) REVERT: B 457 TYR cc_start: 0.8974 (t80) cc_final: 0.8718 (t80) REVERT: B 498 MET cc_start: 0.7821 (ttm) cc_final: 0.7517 (mtt) REVERT: C 14 ARG cc_start: 0.5800 (mmt90) cc_final: 0.5066 (mpt180) REVERT: C 15 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7331 (mm-30) REVERT: C 108 VAL cc_start: 0.9102 (t) cc_final: 0.8811 (t) REVERT: C 185 LEU cc_start: 0.9164 (mt) cc_final: 0.8786 (mp) REVERT: C 219 MET cc_start: 0.7780 (ptm) cc_final: 0.7539 (ptm) REVERT: C 251 MET cc_start: 0.7526 (ttp) cc_final: 0.6921 (ttp) REVERT: C 273 GLN cc_start: 0.8601 (tt0) cc_final: 0.7705 (tt0) REVERT: C 274 MET cc_start: 0.7988 (mmm) cc_final: 0.7754 (mmm) REVERT: C 293 TYR cc_start: 0.8898 (t80) cc_final: 0.8596 (t80) REVERT: C 295 HIS cc_start: 0.8517 (m170) cc_final: 0.8216 (m170) REVERT: C 385 LEU cc_start: 0.8509 (mt) cc_final: 0.8056 (mt) REVERT: C 433 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6321 (tp30) REVERT: C 462 ARG cc_start: 0.8215 (ptm-80) cc_final: 0.7750 (ptm-80) REVERT: D 239 MET cc_start: 0.8348 (mmm) cc_final: 0.8086 (mmm) REVERT: D 247 MET cc_start: 0.8564 (ttp) cc_final: 0.8062 (ttp) REVERT: D 305 GLU cc_start: 0.7399 (tt0) cc_final: 0.7196 (tt0) REVERT: D 311 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7708 (tm-30) REVERT: D 335 THR cc_start: 0.8828 (t) cc_final: 0.8534 (m) REVERT: D 345 HIS cc_start: 0.6745 (t70) cc_final: 0.6406 (t70) REVERT: D 453 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7724 (mm-30) REVERT: D 461 ILE cc_start: 0.8232 (mt) cc_final: 0.8007 (mt) REVERT: E 79 MET cc_start: 0.7854 (mpp) cc_final: 0.7228 (mpp) REVERT: E 128 THR cc_start: 0.7843 (p) cc_final: 0.7495 (p) REVERT: E 251 LEU cc_start: 0.8145 (tp) cc_final: 0.7707 (tp) REVERT: E 264 ASN cc_start: 0.8033 (m110) cc_final: 0.7336 (t0) REVERT: E 279 VAL cc_start: 0.9153 (t) cc_final: 0.8951 (t) REVERT: E 375 LEU cc_start: 0.9168 (tp) cc_final: 0.8844 (tp) REVERT: F 79 MET cc_start: 0.8810 (mmt) cc_final: 0.8307 (mmm) REVERT: F 145 LYS cc_start: 0.8294 (tptp) cc_final: 0.7741 (pttm) REVERT: F 168 ILE cc_start: 0.7779 (mm) cc_final: 0.7293 (mt) REVERT: F 184 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7846 (tp30) REVERT: F 214 MET cc_start: 0.7210 (mmp) cc_final: 0.6877 (tmm) REVERT: F 239 MET cc_start: 0.7211 (ttm) cc_final: 0.6876 (ttm) REVERT: F 247 MET cc_start: 0.7818 (tpt) cc_final: 0.7264 (tpt) REVERT: F 325 GLN cc_start: 0.7131 (pm20) cc_final: 0.6840 (pm20) REVERT: F 393 GLU cc_start: 0.7712 (mp0) cc_final: 0.7417 (mp0) REVERT: F 412 GLU cc_start: 0.4973 (mm-30) cc_final: 0.4400 (tp30) REVERT: F 481 ASP cc_start: 0.7812 (m-30) cc_final: 0.7570 (m-30) REVERT: F 486 LYS cc_start: 0.8994 (tttp) cc_final: 0.8522 (tppp) REVERT: d 98 ASP cc_start: 0.8656 (t0) cc_final: 0.8451 (t0) REVERT: d 104 ARG cc_start: 0.8590 (tpt170) cc_final: 0.8311 (mtm180) REVERT: d 114 PHE cc_start: 0.8584 (t80) cc_final: 0.8336 (t80) REVERT: d 125 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7939 (mttp) REVERT: d 138 LEU cc_start: 0.7386 (mt) cc_final: 0.7169 (mp) REVERT: d 139 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8241 (mp10) REVERT: d 164 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6963 (tp30) REVERT: d 193 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8469 (tt0) REVERT: g 81 ASN cc_start: 0.8249 (t0) cc_final: 0.7958 (t0) REVERT: g 189 LYS cc_start: 0.8643 (mttp) cc_final: 0.8385 (mmmt) REVERT: g 260 LYS cc_start: 0.7924 (pttm) cc_final: 0.7424 (pttp) REVERT: e 11 ASN cc_start: 0.8463 (p0) cc_final: 0.7581 (p0) REVERT: e 18 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7930 (mt-10) REVERT: e 19 VAL cc_start: 0.7874 (t) cc_final: 0.7382 (t) REVERT: e 117 LEU cc_start: 0.8514 (pp) cc_final: 0.7985 (pp) REVERT: e 124 THR cc_start: 0.7937 (m) cc_final: 0.7409 (m) outliers start: 4 outliers final: 0 residues processed: 817 average time/residue: 0.1756 time to fit residues: 226.2252 Evaluate side-chains 555 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 131 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 334 ASN B 342 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076360 restraints weight = 85930.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078612 restraints weight = 48099.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080125 restraints weight = 30581.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081155 restraints weight = 21427.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081879 restraints weight = 16316.345| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27514 Z= 0.176 Angle : 0.716 11.033 37329 Z= 0.365 Chirality : 0.046 0.255 4425 Planarity : 0.005 0.066 4851 Dihedral : 8.244 111.985 4002 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -2.23 (0.14), residues: 3544 helix: -0.32 (0.13), residues: 1477 sheet: -3.22 (0.20), residues: 474 loop : -1.97 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 165 TYR 0.023 0.002 TYR F 213 PHE 0.022 0.002 PHE F 276 TRP 0.015 0.002 TRP e 15 HIS 0.009 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00388 (27513) covalent geometry : angle 0.71582 (37327) SS BOND : bond 0.01848 ( 1) SS BOND : angle 1.45291 ( 2) hydrogen bonds : bond 0.04354 ( 1280) hydrogen bonds : angle 5.64202 ( 3714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 727 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8935 (pt) cc_final: 0.8094 (pt) REVERT: A 63 ILE cc_start: 0.9572 (mm) cc_final: 0.9012 (mm) REVERT: A 137 ILE cc_start: 0.7278 (mp) cc_final: 0.7044 (mp) REVERT: A 251 MET cc_start: 0.7983 (tmm) cc_final: 0.7737 (ttp) REVERT: A 263 ASP cc_start: 0.7861 (t0) cc_final: 0.7658 (t0) REVERT: A 300 GLU cc_start: 0.8847 (tt0) cc_final: 0.7855 (mt-10) REVERT: A 348 ASP cc_start: 0.8727 (p0) cc_final: 0.8397 (p0) REVERT: A 436 MET cc_start: 0.8969 (ppp) cc_final: 0.8450 (ppp) REVERT: A 498 MET cc_start: 0.7967 (mmm) cc_final: 0.7649 (tpt) REVERT: B 14 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8183 (ttp-110) REVERT: B 194 CYS cc_start: 0.8233 (m) cc_final: 0.7839 (m) REVERT: B 266 LYS cc_start: 0.8013 (mptt) cc_final: 0.7810 (mptt) REVERT: B 274 MET cc_start: 0.8910 (ptm) cc_final: 0.8149 (tmm) REVERT: B 293 TYR cc_start: 0.7422 (t80) cc_final: 0.6395 (t80) REVERT: B 386 GLU cc_start: 0.7169 (tp30) cc_final: 0.6893 (tm-30) REVERT: C 14 ARG cc_start: 0.5713 (mmt90) cc_final: 0.4992 (mmt180) REVERT: C 15 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7334 (mm-30) REVERT: C 45 LEU cc_start: 0.8516 (tp) cc_final: 0.8104 (tt) REVERT: C 49 MET cc_start: 0.8311 (tpt) cc_final: 0.7222 (tpt) REVERT: C 105 LEU cc_start: 0.9329 (mp) cc_final: 0.9092 (mp) REVERT: C 165 ARG cc_start: 0.5772 (ptp90) cc_final: 0.5530 (ptp90) REVERT: C 219 MET cc_start: 0.7804 (ptm) cc_final: 0.7593 (ptm) REVERT: C 274 MET cc_start: 0.8062 (mmm) cc_final: 0.7607 (mmm) REVERT: C 293 TYR cc_start: 0.8952 (t80) cc_final: 0.8624 (t80) REVERT: C 385 LEU cc_start: 0.8571 (mt) cc_final: 0.8161 (mt) REVERT: C 462 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7807 (ptm-80) REVERT: D 182 ILE cc_start: 0.8754 (mm) cc_final: 0.7688 (mm) REVERT: D 199 PHE cc_start: 0.8780 (t80) cc_final: 0.8457 (t80) REVERT: D 236 TYR cc_start: 0.4828 (t80) cc_final: 0.4192 (t80) REVERT: D 239 MET cc_start: 0.8359 (mmm) cc_final: 0.7971 (mmm) REVERT: D 247 MET cc_start: 0.8511 (ttp) cc_final: 0.8017 (ttp) REVERT: D 292 MET cc_start: 0.8038 (ttm) cc_final: 0.7499 (ttm) REVERT: D 305 GLU cc_start: 0.7440 (tt0) cc_final: 0.7194 (tt0) REVERT: D 311 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7962 (tm-30) REVERT: D 335 THR cc_start: 0.8784 (t) cc_final: 0.8524 (m) REVERT: D 345 HIS cc_start: 0.6817 (t70) cc_final: 0.5819 (t70) REVERT: D 413 LEU cc_start: 0.8088 (mp) cc_final: 0.7797 (mp) REVERT: D 453 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7765 (mm-30) REVERT: D 469 LEU cc_start: 0.8631 (mt) cc_final: 0.7891 (mt) REVERT: E 64 GLU cc_start: 0.7204 (pm20) cc_final: 0.6854 (pm20) REVERT: E 79 MET cc_start: 0.7947 (mpp) cc_final: 0.7648 (mpp) REVERT: E 128 THR cc_start: 0.7876 (p) cc_final: 0.7568 (p) REVERT: E 183 MET cc_start: 0.8986 (mtt) cc_final: 0.8765 (mtp) REVERT: E 248 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6842 (mmt180) REVERT: E 251 LEU cc_start: 0.8388 (tp) cc_final: 0.8039 (tp) REVERT: E 264 ASN cc_start: 0.8124 (m110) cc_final: 0.7863 (m-40) REVERT: E 283 SER cc_start: 0.8678 (p) cc_final: 0.8433 (t) REVERT: E 299 GLN cc_start: 0.8493 (pm20) cc_final: 0.7777 (pm20) REVERT: E 375 LEU cc_start: 0.9030 (tp) cc_final: 0.8800 (tp) REVERT: E 396 GLN cc_start: 0.8983 (tp40) cc_final: 0.8333 (tp40) REVERT: E 488 MET cc_start: 0.8075 (tmm) cc_final: 0.7641 (tmm) REVERT: F 239 MET cc_start: 0.7141 (ttm) cc_final: 0.6550 (ttm) REVERT: F 247 MET cc_start: 0.7942 (tpt) cc_final: 0.7576 (tpt) REVERT: F 273 ASP cc_start: 0.7904 (p0) cc_final: 0.7657 (p0) REVERT: F 311 GLU cc_start: 0.8031 (tp30) cc_final: 0.7591 (tp30) REVERT: F 343 PHE cc_start: 0.7451 (p90) cc_final: 0.7233 (p90) REVERT: F 412 GLU cc_start: 0.5095 (mm-30) cc_final: 0.4523 (tp30) REVERT: F 481 ASP cc_start: 0.7895 (m-30) cc_final: 0.7540 (m-30) REVERT: F 486 LYS cc_start: 0.9012 (tttp) cc_final: 0.8561 (tppp) REVERT: d 77 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8033 (mtp180) REVERT: d 125 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7960 (mttp) REVERT: d 139 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8545 (mp10) REVERT: d 164 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6656 (tp30) REVERT: d 193 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8436 (tt0) REVERT: g 45 ARG cc_start: 0.6420 (tpp-160) cc_final: 0.5871 (tpp-160) REVERT: g 64 MET cc_start: 0.8297 (tpp) cc_final: 0.7897 (tpp) REVERT: g 81 ASN cc_start: 0.8187 (t0) cc_final: 0.7946 (t0) REVERT: g 189 LYS cc_start: 0.8795 (mttp) cc_final: 0.8463 (mmmt) REVERT: g 287 ASP cc_start: 0.7541 (m-30) cc_final: 0.7324 (m-30) REVERT: g 310 GLU cc_start: 0.8588 (tt0) cc_final: 0.8012 (tp30) REVERT: g 315 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7243 (mm-30) REVERT: g 354 LEU cc_start: 0.8528 (tt) cc_final: 0.8227 (pp) REVERT: e 11 ASN cc_start: 0.8587 (p0) cc_final: 0.7758 (p0) REVERT: e 19 VAL cc_start: 0.8016 (t) cc_final: 0.7655 (t) REVERT: e 117 LEU cc_start: 0.8659 (pp) cc_final: 0.8387 (pp) outliers start: 1 outliers final: 0 residues processed: 727 average time/residue: 0.1706 time to fit residues: 196.6928 Evaluate side-chains 521 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 175 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 12 optimal weight: 0.0030 chunk 187 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 201 GLN B 186 ASN B 342 GLN C 148 GLN C 236 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 247 GLN g 76 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076139 restraints weight = 85487.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078385 restraints weight = 48331.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079838 restraints weight = 30675.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080922 restraints weight = 21670.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081578 restraints weight = 16555.626| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27514 Z= 0.161 Angle : 0.708 11.607 37329 Z= 0.358 Chirality : 0.046 0.249 4425 Planarity : 0.005 0.063 4851 Dihedral : 8.008 111.845 4002 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -1.95 (0.14), residues: 3544 helix: -0.01 (0.13), residues: 1486 sheet: -3.13 (0.20), residues: 492 loop : -1.87 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 172 TYR 0.021 0.002 TYR E 475 PHE 0.031 0.002 PHE A 292 TRP 0.011 0.001 TRP e 15 HIS 0.006 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00361 (27513) covalent geometry : angle 0.70800 (37327) SS BOND : bond 0.02093 ( 1) SS BOND : angle 1.59973 ( 2) hydrogen bonds : bond 0.04163 ( 1280) hydrogen bonds : angle 5.46872 ( 3714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 732 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7182 (tpp) cc_final: 0.6791 (tpp) REVERT: A 263 ASP cc_start: 0.7877 (t0) cc_final: 0.7423 (m-30) REVERT: A 287 TYR cc_start: 0.7742 (m-80) cc_final: 0.7367 (m-10) REVERT: A 300 GLU cc_start: 0.8579 (tt0) cc_final: 0.7427 (mt-10) REVERT: A 348 ASP cc_start: 0.8677 (p0) cc_final: 0.8409 (p0) REVERT: A 436 MET cc_start: 0.8858 (ppp) cc_final: 0.8441 (ppp) REVERT: A 484 GLU cc_start: 0.8403 (mp0) cc_final: 0.7926 (tm-30) REVERT: A 498 MET cc_start: 0.8071 (mmm) cc_final: 0.7714 (tpt) REVERT: B 14 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8087 (ttp-110) REVERT: B 194 CYS cc_start: 0.8167 (m) cc_final: 0.7746 (m) REVERT: B 274 MET cc_start: 0.8929 (ptm) cc_final: 0.8050 (tmm) REVERT: B 293 TYR cc_start: 0.7444 (t80) cc_final: 0.6352 (t80) REVERT: B 298 LEU cc_start: 0.9372 (tt) cc_final: 0.9135 (pp) REVERT: C 15 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7364 (mm-30) REVERT: C 49 MET cc_start: 0.8409 (tpt) cc_final: 0.8051 (tpt) REVERT: C 185 LEU cc_start: 0.9136 (mt) cc_final: 0.8916 (mt) REVERT: C 262 ASP cc_start: 0.7732 (p0) cc_final: 0.7240 (p0) REVERT: C 266 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7934 (mmtt) REVERT: C 293 TYR cc_start: 0.8952 (t80) cc_final: 0.8455 (t80) REVERT: C 313 SER cc_start: 0.7150 (p) cc_final: 0.6493 (p) REVERT: D 63 CYS cc_start: 0.8129 (m) cc_final: 0.7832 (m) REVERT: D 236 TYR cc_start: 0.4573 (t80) cc_final: 0.4166 (t80) REVERT: D 239 MET cc_start: 0.8400 (mmm) cc_final: 0.7927 (mmt) REVERT: D 247 MET cc_start: 0.8493 (ttp) cc_final: 0.7850 (ttm) REVERT: D 335 THR cc_start: 0.8821 (t) cc_final: 0.8538 (m) REVERT: D 345 HIS cc_start: 0.6706 (t70) cc_final: 0.6101 (t70) REVERT: D 453 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7763 (mm-30) REVERT: E 79 MET cc_start: 0.7853 (mpp) cc_final: 0.7625 (mpp) REVERT: E 128 THR cc_start: 0.7892 (p) cc_final: 0.7632 (p) REVERT: E 236 TYR cc_start: 0.6768 (t80) cc_final: 0.6465 (t80) REVERT: E 283 SER cc_start: 0.8681 (p) cc_final: 0.8436 (t) REVERT: E 299 GLN cc_start: 0.8429 (pm20) cc_final: 0.7713 (pm20) REVERT: E 375 LEU cc_start: 0.8979 (tp) cc_final: 0.8726 (tp) REVERT: E 398 TYR cc_start: 0.8163 (t80) cc_final: 0.7935 (t80) REVERT: E 428 GLU cc_start: 0.8124 (pt0) cc_final: 0.7808 (pt0) REVERT: E 429 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7679 (mtm-85) REVERT: F 213 TYR cc_start: 0.8397 (t80) cc_final: 0.7941 (t80) REVERT: F 239 MET cc_start: 0.7226 (ttm) cc_final: 0.6664 (ttm) REVERT: F 273 ASP cc_start: 0.8109 (p0) cc_final: 0.7700 (p0) REVERT: F 328 TYR cc_start: 0.8111 (t80) cc_final: 0.7868 (t80) REVERT: F 412 GLU cc_start: 0.5202 (mm-30) cc_final: 0.4734 (tp30) REVERT: F 481 ASP cc_start: 0.7957 (m-30) cc_final: 0.7629 (m-30) REVERT: F 486 LYS cc_start: 0.8987 (tttp) cc_final: 0.8556 (tppp) REVERT: d 77 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8035 (mtp180) REVERT: d 112 TYR cc_start: 0.7881 (t80) cc_final: 0.7519 (t80) REVERT: d 114 PHE cc_start: 0.8768 (t80) cc_final: 0.8548 (t80) REVERT: d 125 LYS cc_start: 0.8271 (mtpt) cc_final: 0.8010 (mttp) REVERT: d 139 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8534 (mp10) REVERT: d 164 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7082 (tp30) REVERT: d 193 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8473 (tt0) REVERT: g 45 ARG cc_start: 0.6370 (tpp-160) cc_final: 0.5926 (tpp-160) REVERT: g 64 MET cc_start: 0.8265 (tpp) cc_final: 0.7971 (tpp) REVERT: g 180 PHE cc_start: 0.7063 (t80) cc_final: 0.6804 (t80) REVERT: g 189 LYS cc_start: 0.8816 (mttp) cc_final: 0.8451 (mmmt) REVERT: g 303 GLN cc_start: 0.8548 (tp40) cc_final: 0.8209 (tp40) REVERT: g 354 LEU cc_start: 0.8531 (tt) cc_final: 0.8249 (pp) REVERT: e 11 ASN cc_start: 0.8576 (p0) cc_final: 0.7969 (p0) REVERT: e 19 VAL cc_start: 0.8106 (t) cc_final: 0.7776 (t) REVERT: e 124 THR cc_start: 0.7594 (m) cc_final: 0.7382 (m) outliers start: 1 outliers final: 0 residues processed: 733 average time/residue: 0.1686 time to fit residues: 197.1362 Evaluate side-chains 510 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 179 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 0.0770 chunk 86 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 342 GLN B 186 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 433 GLN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN F 396 GLN F 472 GLN g 243 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077341 restraints weight = 84484.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079601 restraints weight = 48182.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081129 restraints weight = 30762.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082179 restraints weight = 21696.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082836 restraints weight = 16581.126| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27514 Z= 0.147 Angle : 0.714 13.033 37329 Z= 0.356 Chirality : 0.046 0.258 4425 Planarity : 0.005 0.065 4851 Dihedral : 7.879 114.588 4002 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -1.73 (0.14), residues: 3544 helix: 0.15 (0.13), residues: 1478 sheet: -3.02 (0.21), residues: 471 loop : -1.73 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 172 TYR 0.024 0.002 TYR D 298 PHE 0.029 0.002 PHE A 292 TRP 0.009 0.002 TRP e 15 HIS 0.004 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00329 (27513) covalent geometry : angle 0.71417 (37327) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.88706 ( 2) hydrogen bonds : bond 0.03997 ( 1280) hydrogen bonds : angle 5.40583 ( 3714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7208 (tpp) cc_final: 0.6684 (tpp) REVERT: A 230 ASP cc_start: 0.7573 (p0) cc_final: 0.7087 (p0) REVERT: A 263 ASP cc_start: 0.7711 (t0) cc_final: 0.7089 (m-30) REVERT: A 287 TYR cc_start: 0.7790 (m-80) cc_final: 0.7490 (m-80) REVERT: A 300 GLU cc_start: 0.8323 (tt0) cc_final: 0.7907 (mt-10) REVERT: A 348 ASP cc_start: 0.8725 (p0) cc_final: 0.8376 (p0) REVERT: A 436 MET cc_start: 0.8813 (ppp) cc_final: 0.8345 (ppp) REVERT: A 484 GLU cc_start: 0.8444 (mp0) cc_final: 0.7897 (tm-30) REVERT: A 498 MET cc_start: 0.8269 (tpt) cc_final: 0.7751 (tpt) REVERT: B 68 GLU cc_start: 0.7958 (tp30) cc_final: 0.7403 (tm-30) REVERT: B 171 ASP cc_start: 0.7594 (t0) cc_final: 0.7389 (t70) REVERT: B 194 CYS cc_start: 0.8056 (m) cc_final: 0.7697 (m) REVERT: B 274 MET cc_start: 0.8942 (ptm) cc_final: 0.8024 (tmm) REVERT: B 293 TYR cc_start: 0.7414 (t80) cc_final: 0.6336 (t80) REVERT: C 15 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7349 (mm-30) REVERT: C 45 LEU cc_start: 0.8612 (tp) cc_final: 0.8252 (tt) REVERT: C 49 MET cc_start: 0.8402 (tpt) cc_final: 0.7322 (tpt) REVERT: C 105 LEU cc_start: 0.9315 (mp) cc_final: 0.9007 (mp) REVERT: C 165 ARG cc_start: 0.5358 (ptp90) cc_final: 0.5126 (ptp-170) REVERT: C 172 ARG cc_start: 0.6760 (mtt180) cc_final: 0.6465 (mtt180) REVERT: C 259 ILE cc_start: 0.8862 (pt) cc_final: 0.8452 (pt) REVERT: C 266 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8091 (mmtt) REVERT: C 274 MET cc_start: 0.7740 (mmm) cc_final: 0.7417 (mmm) REVERT: C 293 TYR cc_start: 0.8956 (t80) cc_final: 0.8536 (t80) REVERT: C 365 SER cc_start: 0.9088 (p) cc_final: 0.8834 (p) REVERT: C 385 LEU cc_start: 0.8580 (mt) cc_final: 0.8298 (mt) REVERT: D 236 TYR cc_start: 0.4695 (t80) cc_final: 0.4211 (t80) REVERT: D 239 MET cc_start: 0.8319 (mmm) cc_final: 0.7883 (mmt) REVERT: D 247 MET cc_start: 0.8446 (ttp) cc_final: 0.7958 (ttp) REVERT: D 292 MET cc_start: 0.8018 (ttm) cc_final: 0.7535 (ttm) REVERT: D 305 GLU cc_start: 0.6930 (tt0) cc_final: 0.6660 (tt0) REVERT: D 335 THR cc_start: 0.8819 (t) cc_final: 0.8591 (m) REVERT: D 453 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7736 (mm-30) REVERT: E 22 ARG cc_start: 0.7370 (mmp80) cc_final: 0.7101 (mmp80) REVERT: E 64 GLU cc_start: 0.6944 (pm20) cc_final: 0.6429 (pm20) REVERT: E 128 THR cc_start: 0.7835 (p) cc_final: 0.6873 (p) REVERT: E 236 TYR cc_start: 0.6728 (t80) cc_final: 0.6520 (t80) REVERT: E 279 VAL cc_start: 0.9058 (t) cc_final: 0.8853 (t) REVERT: E 299 GLN cc_start: 0.8366 (pm20) cc_final: 0.7562 (pm20) REVERT: E 375 LEU cc_start: 0.9027 (tp) cc_final: 0.8816 (tp) REVERT: E 398 TYR cc_start: 0.8184 (t80) cc_final: 0.7867 (t80) REVERT: E 475 TYR cc_start: 0.8056 (t80) cc_final: 0.7827 (t80) REVERT: F 79 MET cc_start: 0.8886 (mmt) cc_final: 0.8277 (mmm) REVERT: F 82 THR cc_start: 0.7901 (p) cc_final: 0.7685 (p) REVERT: F 213 TYR cc_start: 0.8442 (t80) cc_final: 0.7982 (t80) REVERT: F 239 MET cc_start: 0.6973 (ttm) cc_final: 0.6392 (ttm) REVERT: F 343 PHE cc_start: 0.7614 (p90) cc_final: 0.7333 (p90) REVERT: F 412 GLU cc_start: 0.5316 (mm-30) cc_final: 0.4935 (tp30) REVERT: F 481 ASP cc_start: 0.7996 (m-30) cc_final: 0.7718 (m-30) REVERT: F 486 LYS cc_start: 0.8986 (tttp) cc_final: 0.8506 (tppp) REVERT: d 77 ARG cc_start: 0.8513 (mtp180) cc_final: 0.8090 (mtp180) REVERT: d 139 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8454 (mp10) REVERT: d 151 ASP cc_start: 0.8289 (m-30) cc_final: 0.7532 (m-30) REVERT: d 164 GLU cc_start: 0.7835 (mm-30) cc_final: 0.6394 (tp30) REVERT: d 167 ASP cc_start: 0.7965 (t70) cc_final: 0.7652 (t70) REVERT: d 193 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8457 (tt0) REVERT: g 189 LYS cc_start: 0.8783 (mttp) cc_final: 0.8516 (mmmt) REVERT: g 303 GLN cc_start: 0.8571 (tp40) cc_final: 0.8220 (tp40) REVERT: g 310 GLU cc_start: 0.8548 (tt0) cc_final: 0.7978 (tp30) REVERT: g 320 MET cc_start: 0.7158 (ttt) cc_final: 0.6070 (tmm) REVERT: g 354 LEU cc_start: 0.8426 (tt) cc_final: 0.8129 (pp) REVERT: e 19 VAL cc_start: 0.8029 (t) cc_final: 0.7702 (t) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.1640 time to fit residues: 188.2356 Evaluate side-chains 499 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 286 optimal weight: 10.0000 chunk 204 optimal weight: 0.0470 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 216 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 chunk 315 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 0.0060 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 497 GLN D 25 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN F 280 GLN F 299 GLN F 472 GLN d 141 HIS g 243 ASN g 301 ASN g 309 GLN e 56 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078540 restraints weight = 84507.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080822 restraints weight = 47973.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082361 restraints weight = 30773.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083320 restraints weight = 21639.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084095 restraints weight = 16791.698| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27514 Z= 0.138 Angle : 0.714 13.019 37329 Z= 0.357 Chirality : 0.046 0.272 4425 Planarity : 0.005 0.084 4851 Dihedral : 7.739 117.169 4002 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 1.37 % Twisted General : 0.06 % 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: -1.64 (0.14), residues: 3544 helix: 0.20 (0.13), residues: 1497 sheet: -2.89 (0.22), residues: 479 loop : -1.71 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 280 TYR 0.026 0.002 TYR E 298 PHE 0.027 0.002 PHE D 343 TRP 0.009 0.002 TRP e 15 HIS 0.005 0.001 HIS g 228 Details of bonding type rmsd covalent geometry : bond 0.00306 (27513) covalent geometry : angle 0.71412 (37327) SS BOND : bond 0.00139 ( 1) SS BOND : angle 1.40599 ( 2) hydrogen bonds : bond 0.03918 ( 1280) hydrogen bonds : angle 5.34208 ( 3714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8786 (pt) cc_final: 0.8031 (mp) REVERT: A 157 MET cc_start: 0.7829 (ttm) cc_final: 0.7606 (ttm) REVERT: A 296 SER cc_start: 0.8516 (t) cc_final: 0.6862 (t) REVERT: A 300 GLU cc_start: 0.8299 (tt0) cc_final: 0.7790 (mt-10) REVERT: A 348 ASP cc_start: 0.8723 (p0) cc_final: 0.8340 (p0) REVERT: A 436 MET cc_start: 0.8801 (ppp) cc_final: 0.8411 (ppp) REVERT: A 484 GLU cc_start: 0.8447 (mp0) cc_final: 0.7911 (tm-30) REVERT: A 498 MET cc_start: 0.8262 (tpt) cc_final: 0.7726 (tpt) REVERT: B 34 GLN cc_start: 0.7644 (tp-100) cc_final: 0.6891 (tt0) REVERT: B 147 LEU cc_start: 0.8515 (tt) cc_final: 0.8016 (tt) REVERT: B 148 GLN cc_start: 0.8155 (mp10) cc_final: 0.7946 (mp10) REVERT: B 149 THR cc_start: 0.9356 (p) cc_final: 0.9135 (t) REVERT: B 194 CYS cc_start: 0.7930 (m) cc_final: 0.7484 (m) REVERT: B 274 MET cc_start: 0.8910 (ptm) cc_final: 0.7889 (tmm) REVERT: B 293 TYR cc_start: 0.7381 (t80) cc_final: 0.6335 (t80) REVERT: B 298 LEU cc_start: 0.9337 (tt) cc_final: 0.9088 (pp) REVERT: C 15 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7329 (mm-30) REVERT: C 49 MET cc_start: 0.8489 (tpt) cc_final: 0.8080 (tpt) REVERT: C 219 MET cc_start: 0.7973 (ptt) cc_final: 0.7733 (ptt) REVERT: C 266 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7970 (mmtt) REVERT: C 274 MET cc_start: 0.7805 (mmm) cc_final: 0.7502 (mmm) REVERT: C 293 TYR cc_start: 0.8963 (t80) cc_final: 0.8551 (t80) REVERT: C 314 MET cc_start: 0.7910 (tpt) cc_final: 0.7613 (tpp) REVERT: C 365 SER cc_start: 0.8955 (p) cc_final: 0.8739 (p) REVERT: C 385 LEU cc_start: 0.8589 (mt) cc_final: 0.8276 (mt) REVERT: C 484 GLU cc_start: 0.8218 (tp30) cc_final: 0.7948 (tp30) REVERT: D 63 CYS cc_start: 0.8002 (m) cc_final: 0.7721 (m) REVERT: D 236 TYR cc_start: 0.4603 (t80) cc_final: 0.4170 (t80) REVERT: D 239 MET cc_start: 0.8342 (mmm) cc_final: 0.7952 (mmt) REVERT: D 247 MET cc_start: 0.8376 (ttp) cc_final: 0.7870 (ttp) REVERT: D 285 VAL cc_start: 0.9419 (t) cc_final: 0.9219 (t) REVERT: D 292 MET cc_start: 0.7983 (ttm) cc_final: 0.7517 (ttm) REVERT: D 335 THR cc_start: 0.8847 (t) cc_final: 0.8607 (m) REVERT: D 453 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7687 (mm-30) REVERT: E 22 ARG cc_start: 0.7381 (mmp80) cc_final: 0.7057 (mmp80) REVERT: E 79 MET cc_start: 0.7791 (mpp) cc_final: 0.7555 (mpp) REVERT: E 182 ILE cc_start: 0.9229 (mm) cc_final: 0.8949 (mt) REVERT: E 199 PHE cc_start: 0.8444 (t80) cc_final: 0.8230 (t80) REVERT: E 236 TYR cc_start: 0.6727 (t80) cc_final: 0.6381 (t80) REVERT: E 299 GLN cc_start: 0.7923 (pm20) cc_final: 0.7263 (pm20) REVERT: E 398 TYR cc_start: 0.8155 (t80) cc_final: 0.7849 (t80) REVERT: E 475 TYR cc_start: 0.8024 (t80) cc_final: 0.7756 (t80) REVERT: F 79 MET cc_start: 0.8919 (mmt) cc_final: 0.8323 (mmm) REVERT: F 213 TYR cc_start: 0.8439 (t80) cc_final: 0.8083 (t80) REVERT: F 239 MET cc_start: 0.6911 (ttm) cc_final: 0.6690 (ttm) REVERT: F 247 MET cc_start: 0.8022 (tpp) cc_final: 0.7569 (tpt) REVERT: F 254 LEU cc_start: 0.8719 (tp) cc_final: 0.8443 (tp) REVERT: F 343 PHE cc_start: 0.7720 (p90) cc_final: 0.7388 (p90) REVERT: F 374 MET cc_start: 0.8780 (mmt) cc_final: 0.8458 (mpp) REVERT: F 481 ASP cc_start: 0.8052 (m-30) cc_final: 0.7770 (m-30) REVERT: F 486 LYS cc_start: 0.8964 (tttp) cc_final: 0.8517 (tppp) REVERT: d 77 ARG cc_start: 0.8467 (mtp180) cc_final: 0.7960 (mtp180) REVERT: d 104 ARG cc_start: 0.8602 (tpt170) cc_final: 0.8246 (mtm180) REVERT: d 139 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8447 (mp10) REVERT: d 149 LEU cc_start: 0.8941 (mm) cc_final: 0.8531 (tp) REVERT: d 164 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6266 (tp30) REVERT: d 167 ASP cc_start: 0.7980 (t70) cc_final: 0.7663 (t70) REVERT: d 193 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8443 (tt0) REVERT: d 205 LYS cc_start: 0.8195 (pttp) cc_final: 0.7642 (mmmt) REVERT: g 46 GLU cc_start: 0.7431 (mp0) cc_final: 0.6539 (pp20) REVERT: g 303 GLN cc_start: 0.8514 (tp40) cc_final: 0.8243 (tp40) REVERT: g 354 LEU cc_start: 0.8474 (tt) cc_final: 0.8109 (pp) REVERT: e 11 ASN cc_start: 0.8618 (p0) cc_final: 0.8091 (p0) REVERT: e 19 VAL cc_start: 0.8131 (t) cc_final: 0.7830 (t) outliers start: 1 outliers final: 0 residues processed: 706 average time/residue: 0.1626 time to fit residues: 186.1554 Evaluate side-chains 516 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 342 GLN B 186 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 188 ASN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 240 ASN F 299 GLN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 ASN g 243 ASN g 301 ASN e 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077919 restraints weight = 84487.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080189 restraints weight = 47977.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081728 restraints weight = 30859.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082801 restraints weight = 21809.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083487 restraints weight = 16648.610| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27514 Z= 0.150 Angle : 0.725 13.810 37329 Z= 0.362 Chirality : 0.047 0.275 4425 Planarity : 0.005 0.097 4851 Dihedral : 7.696 116.565 4002 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 1.37 % Twisted General : 0.06 % 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: -1.59 (0.14), residues: 3544 helix: 0.21 (0.13), residues: 1505 sheet: -2.85 (0.22), residues: 485 loop : -1.65 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 378 TYR 0.024 0.002 TYR E 385 PHE 0.032 0.002 PHE A 292 TRP 0.007 0.002 TRP e 57 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00341 (27513) covalent geometry : angle 0.72535 (37327) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.34980 ( 2) hydrogen bonds : bond 0.03937 ( 1280) hydrogen bonds : angle 5.31395 ( 3714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7825 (ttm) cc_final: 0.7525 (ttm) REVERT: A 238 LEU cc_start: 0.8337 (mt) cc_final: 0.8066 (mt) REVERT: A 296 SER cc_start: 0.8509 (t) cc_final: 0.7283 (t) REVERT: A 300 GLU cc_start: 0.8330 (tt0) cc_final: 0.7722 (mt-10) REVERT: A 348 ASP cc_start: 0.8806 (p0) cc_final: 0.8423 (p0) REVERT: A 436 MET cc_start: 0.8812 (ppp) cc_final: 0.8509 (ppp) REVERT: A 484 GLU cc_start: 0.8491 (mp0) cc_final: 0.7765 (tm-30) REVERT: A 498 MET cc_start: 0.8274 (tpt) cc_final: 0.7714 (tpt) REVERT: B 25 LYS cc_start: 0.7117 (pttp) cc_final: 0.6644 (mtpt) REVERT: B 147 LEU cc_start: 0.8609 (tt) cc_final: 0.8067 (tt) REVERT: B 148 GLN cc_start: 0.8274 (mp10) cc_final: 0.8010 (mp10) REVERT: B 274 MET cc_start: 0.8996 (ptm) cc_final: 0.7956 (tmm) REVERT: B 293 TYR cc_start: 0.7403 (t80) cc_final: 0.6414 (t80) REVERT: B 298 LEU cc_start: 0.9325 (tt) cc_final: 0.8978 (pp) REVERT: C 15 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7328 (mm-30) REVERT: C 45 LEU cc_start: 0.8676 (tp) cc_final: 0.8307 (tt) REVERT: C 49 MET cc_start: 0.8530 (tpt) cc_final: 0.8213 (tpt) REVERT: C 105 LEU cc_start: 0.9301 (mp) cc_final: 0.8957 (mp) REVERT: C 219 MET cc_start: 0.7982 (ptt) cc_final: 0.7683 (ptm) REVERT: C 266 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7911 (mmtt) REVERT: C 274 MET cc_start: 0.7941 (mmm) cc_final: 0.7439 (mmm) REVERT: C 293 TYR cc_start: 0.8959 (t80) cc_final: 0.8522 (t80) REVERT: C 314 MET cc_start: 0.7998 (tpt) cc_final: 0.7520 (tpp) REVERT: C 385 LEU cc_start: 0.8593 (mt) cc_final: 0.8302 (mt) REVERT: C 484 GLU cc_start: 0.8153 (tp30) cc_final: 0.7885 (tp30) REVERT: D 63 CYS cc_start: 0.8092 (m) cc_final: 0.7833 (m) REVERT: D 133 HIS cc_start: 0.5978 (t-90) cc_final: 0.5701 (t-90) REVERT: D 182 ILE cc_start: 0.9152 (mm) cc_final: 0.8936 (mm) REVERT: D 236 TYR cc_start: 0.4698 (t80) cc_final: 0.4288 (t80) REVERT: D 239 MET cc_start: 0.8345 (mmm) cc_final: 0.7960 (mmt) REVERT: D 247 MET cc_start: 0.8366 (ttp) cc_final: 0.7882 (ttp) REVERT: D 292 MET cc_start: 0.8062 (ttm) cc_final: 0.7583 (ttm) REVERT: D 342 THR cc_start: 0.8059 (p) cc_final: 0.7859 (p) REVERT: D 366 ASP cc_start: 0.8036 (t0) cc_final: 0.6877 (t0) REVERT: D 453 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 469 LEU cc_start: 0.8638 (mt) cc_final: 0.8434 (mt) REVERT: E 22 ARG cc_start: 0.7330 (mmp80) cc_final: 0.6978 (mmp80) REVERT: E 64 GLU cc_start: 0.6866 (pm20) cc_final: 0.6452 (pm20) REVERT: E 277 ARG cc_start: 0.8627 (tpp-160) cc_final: 0.8087 (mmp80) REVERT: E 283 SER cc_start: 0.8937 (t) cc_final: 0.8643 (t) REVERT: E 299 GLN cc_start: 0.7980 (pm20) cc_final: 0.7182 (pm20) REVERT: E 398 TYR cc_start: 0.8125 (t80) cc_final: 0.7873 (t80) REVERT: E 428 GLU cc_start: 0.8113 (pt0) cc_final: 0.7868 (pt0) REVERT: E 475 TYR cc_start: 0.8073 (t80) cc_final: 0.7773 (t80) REVERT: F 79 MET cc_start: 0.8903 (mmt) cc_final: 0.8476 (mmm) REVERT: F 239 MET cc_start: 0.7070 (ttm) cc_final: 0.6772 (ttm) REVERT: F 254 LEU cc_start: 0.8734 (tp) cc_final: 0.8489 (tp) REVERT: F 374 MET cc_start: 0.8747 (mmt) cc_final: 0.8523 (mpp) REVERT: F 486 LYS cc_start: 0.8992 (tttp) cc_final: 0.8530 (tppp) REVERT: d 77 ARG cc_start: 0.8493 (mtp180) cc_final: 0.7943 (mtp180) REVERT: d 139 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8425 (mp10) REVERT: d 157 LEU cc_start: 0.9255 (mt) cc_final: 0.8745 (mt) REVERT: d 162 LEU cc_start: 0.8894 (mt) cc_final: 0.8368 (tt) REVERT: d 164 GLU cc_start: 0.7814 (mm-30) cc_final: 0.6517 (tp30) REVERT: d 193 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8488 (tt0) REVERT: d 205 LYS cc_start: 0.8240 (pttp) cc_final: 0.7808 (mmmt) REVERT: g 71 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8411 (mmmm) REVERT: g 121 MET cc_start: 0.7272 (ppp) cc_final: 0.6946 (tmm) REVERT: g 303 GLN cc_start: 0.8543 (tp40) cc_final: 0.8282 (tp40) REVERT: g 354 LEU cc_start: 0.8454 (tt) cc_final: 0.8080 (pp) REVERT: e 11 ASN cc_start: 0.8540 (p0) cc_final: 0.8041 (p0) REVERT: e 19 VAL cc_start: 0.8090 (t) cc_final: 0.7774 (t) outliers start: 1 outliers final: 1 residues processed: 683 average time/residue: 0.1629 time to fit residues: 181.1226 Evaluate side-chains 501 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 305 optimal weight: 9.9990 chunk 289 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 164 optimal weight: 0.0670 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 188 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN E 240 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN F 299 GLN F 402 GLN d 141 HIS g 243 ASN g 301 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078553 restraints weight = 84547.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080821 restraints weight = 48055.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082349 restraints weight = 30937.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083315 restraints weight = 21887.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084070 restraints weight = 16999.905| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27514 Z= 0.140 Angle : 0.728 14.205 37329 Z= 0.363 Chirality : 0.046 0.303 4425 Planarity : 0.005 0.067 4851 Dihedral : 7.588 117.876 4002 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.48 (0.14), residues: 3544 helix: 0.30 (0.13), residues: 1498 sheet: -2.76 (0.22), residues: 466 loop : -1.62 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 462 TYR 0.025 0.002 TYR E 385 PHE 0.028 0.002 PHE A 292 TRP 0.006 0.001 TRP e 15 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00318 (27513) covalent geometry : angle 0.72820 (37327) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.99618 ( 2) hydrogen bonds : bond 0.03913 ( 1280) hydrogen bonds : angle 5.25557 ( 3714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 679 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8657 (pt) cc_final: 0.8384 (pt) REVERT: A 157 MET cc_start: 0.7840 (ttm) cc_final: 0.7583 (ttm) REVERT: A 220 GLU cc_start: 0.8054 (pt0) cc_final: 0.7674 (pm20) REVERT: A 238 LEU cc_start: 0.8361 (mt) cc_final: 0.8086 (mt) REVERT: A 296 SER cc_start: 0.8488 (t) cc_final: 0.7402 (t) REVERT: A 300 GLU cc_start: 0.8311 (tt0) cc_final: 0.7856 (mt-10) REVERT: A 348 ASP cc_start: 0.8828 (p0) cc_final: 0.8487 (p0) REVERT: A 360 VAL cc_start: 0.7812 (m) cc_final: 0.7572 (m) REVERT: A 436 MET cc_start: 0.8830 (ppp) cc_final: 0.8461 (ppp) REVERT: A 484 GLU cc_start: 0.8454 (mp0) cc_final: 0.7805 (tm-30) REVERT: B 34 GLN cc_start: 0.7717 (tp-100) cc_final: 0.6839 (tt0) REVERT: B 147 LEU cc_start: 0.8547 (tt) cc_final: 0.8021 (tt) REVERT: B 148 GLN cc_start: 0.8133 (mp10) cc_final: 0.7925 (mp10) REVERT: B 149 THR cc_start: 0.9413 (p) cc_final: 0.9134 (t) REVERT: B 194 CYS cc_start: 0.7972 (m) cc_final: 0.7729 (m) REVERT: B 274 MET cc_start: 0.8919 (ptm) cc_final: 0.7974 (tmm) REVERT: B 293 TYR cc_start: 0.7366 (t80) cc_final: 0.6400 (t80) REVERT: B 298 LEU cc_start: 0.9336 (tt) cc_final: 0.8976 (pp) REVERT: C 45 LEU cc_start: 0.8713 (tp) cc_final: 0.8404 (tt) REVERT: C 49 MET cc_start: 0.8520 (tpt) cc_final: 0.8169 (tpt) REVERT: C 105 LEU cc_start: 0.9315 (mp) cc_final: 0.9009 (mp) REVERT: C 114 LYS cc_start: 0.8588 (tptp) cc_final: 0.8354 (tptm) REVERT: C 115 PRO cc_start: 0.8520 (Cg_exo) cc_final: 0.8279 (Cg_endo) REVERT: C 172 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6515 (mtt180) REVERT: C 219 MET cc_start: 0.7917 (ptt) cc_final: 0.7622 (ptm) REVERT: C 251 MET cc_start: 0.7406 (tmm) cc_final: 0.6992 (tmm) REVERT: C 266 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7839 (mmtt) REVERT: C 274 MET cc_start: 0.7957 (mmm) cc_final: 0.7440 (mmm) REVERT: C 314 MET cc_start: 0.8055 (tpt) cc_final: 0.7046 (tpp) REVERT: C 365 SER cc_start: 0.9083 (p) cc_final: 0.8868 (p) REVERT: C 385 LEU cc_start: 0.8572 (mt) cc_final: 0.8287 (mt) REVERT: C 484 GLU cc_start: 0.8079 (tp30) cc_final: 0.7841 (tp30) REVERT: D 42 ASN cc_start: 0.8014 (m-40) cc_final: 0.7780 (t0) REVERT: D 63 CYS cc_start: 0.8153 (m) cc_final: 0.7861 (m) REVERT: D 236 TYR cc_start: 0.4664 (t80) cc_final: 0.4330 (t80) REVERT: D 239 MET cc_start: 0.8317 (mmm) cc_final: 0.7971 (mmt) REVERT: D 247 MET cc_start: 0.8303 (ttp) cc_final: 0.7895 (ttp) REVERT: D 285 VAL cc_start: 0.9519 (t) cc_final: 0.9299 (t) REVERT: D 292 MET cc_start: 0.7995 (ttm) cc_final: 0.7510 (ttm) REVERT: D 342 THR cc_start: 0.7954 (p) cc_final: 0.7656 (p) REVERT: D 366 ASP cc_start: 0.8072 (t0) cc_final: 0.7035 (t0) REVERT: D 453 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 469 LEU cc_start: 0.8614 (mt) cc_final: 0.8381 (mt) REVERT: E 22 ARG cc_start: 0.7439 (mmp80) cc_final: 0.7107 (mmp80) REVERT: E 64 GLU cc_start: 0.6910 (pm20) cc_final: 0.6483 (pm20) REVERT: E 79 MET cc_start: 0.7680 (mpp) cc_final: 0.7295 (mpp) REVERT: E 80 SER cc_start: 0.9131 (m) cc_final: 0.8605 (t) REVERT: E 283 SER cc_start: 0.8886 (t) cc_final: 0.8642 (t) REVERT: E 299 GLN cc_start: 0.7859 (pm20) cc_final: 0.7215 (pm20) REVERT: E 393 GLU cc_start: 0.7940 (tp30) cc_final: 0.7739 (tp30) REVERT: E 398 TYR cc_start: 0.8089 (t80) cc_final: 0.7863 (t80) REVERT: E 428 GLU cc_start: 0.8017 (pt0) cc_final: 0.7663 (pt0) REVERT: E 475 TYR cc_start: 0.8080 (t80) cc_final: 0.7767 (t80) REVERT: F 25 GLN cc_start: 0.7211 (tt0) cc_final: 0.6819 (tt0) REVERT: F 32 ASP cc_start: 0.6610 (m-30) cc_final: 0.5886 (m-30) REVERT: F 239 MET cc_start: 0.7038 (ttm) cc_final: 0.6519 (ttm) REVERT: F 251 LEU cc_start: 0.8192 (mp) cc_final: 0.7795 (mp) REVERT: F 486 LYS cc_start: 0.9015 (tttp) cc_final: 0.8577 (tppp) REVERT: d 104 ARG cc_start: 0.8646 (tpt170) cc_final: 0.8350 (mtm180) REVERT: d 139 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8345 (mp10) REVERT: d 155 ILE cc_start: 0.8953 (tt) cc_final: 0.8744 (tt) REVERT: d 164 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6137 (tp30) REVERT: d 205 LYS cc_start: 0.8216 (pttp) cc_final: 0.7864 (mmmt) REVERT: d 234 ASP cc_start: 0.7330 (p0) cc_final: 0.7016 (p0) REVERT: d 238 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7795 (mtmt) REVERT: g 121 MET cc_start: 0.7386 (ppp) cc_final: 0.6003 (tmm) REVERT: g 302 SER cc_start: 0.9176 (t) cc_final: 0.8960 (t) REVERT: g 303 GLN cc_start: 0.8568 (tp40) cc_final: 0.8274 (tp40) REVERT: g 310 GLU cc_start: 0.8764 (tp30) cc_final: 0.8316 (tp30) REVERT: g 354 LEU cc_start: 0.8432 (tt) cc_final: 0.8092 (pp) REVERT: e 11 ASN cc_start: 0.8558 (p0) cc_final: 0.8027 (p0) REVERT: e 19 VAL cc_start: 0.8104 (t) cc_final: 0.7833 (t) outliers start: 2 outliers final: 0 residues processed: 680 average time/residue: 0.1644 time to fit residues: 181.3494 Evaluate side-chains 509 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 97 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 chunk 223 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 256 HIS B 186 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN g 97 ASN g 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078800 restraints weight = 84601.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081060 restraints weight = 48230.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082546 restraints weight = 31124.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083622 restraints weight = 22171.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.084283 restraints weight = 16985.886| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27514 Z= 0.145 Angle : 0.727 15.184 37329 Z= 0.362 Chirality : 0.047 0.308 4425 Planarity : 0.005 0.080 4851 Dihedral : 7.530 118.991 4002 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.44 (0.14), residues: 3544 helix: 0.31 (0.13), residues: 1503 sheet: -2.67 (0.23), residues: 469 loop : -1.60 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 418 TYR 0.033 0.002 TYR E 298 PHE 0.035 0.002 PHE B 390 TRP 0.006 0.001 TRP e 15 HIS 0.005 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00330 (27513) covalent geometry : angle 0.72741 (37327) SS BOND : bond 0.00216 ( 1) SS BOND : angle 1.06232 ( 2) hydrogen bonds : bond 0.03918 ( 1280) hydrogen bonds : angle 5.21955 ( 3714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7829 (ttm) cc_final: 0.7527 (ttm) REVERT: A 219 MET cc_start: 0.7451 (ppp) cc_final: 0.7152 (ppp) REVERT: A 220 GLU cc_start: 0.8130 (pt0) cc_final: 0.7616 (pm20) REVERT: A 238 LEU cc_start: 0.8143 (mt) cc_final: 0.7777 (mt) REVERT: A 296 SER cc_start: 0.8480 (t) cc_final: 0.7289 (t) REVERT: A 300 GLU cc_start: 0.8354 (tt0) cc_final: 0.7889 (mt-10) REVERT: A 348 ASP cc_start: 0.8863 (p0) cc_final: 0.8547 (p0) REVERT: A 436 MET cc_start: 0.8871 (ppp) cc_final: 0.8592 (ppp) REVERT: A 484 GLU cc_start: 0.8491 (mp0) cc_final: 0.7836 (tm-30) REVERT: B 147 LEU cc_start: 0.8574 (tt) cc_final: 0.8024 (tt) REVERT: B 148 GLN cc_start: 0.8200 (mp10) cc_final: 0.7985 (mp10) REVERT: B 149 THR cc_start: 0.9401 (p) cc_final: 0.9070 (t) REVERT: B 169 ILE cc_start: 0.9269 (tp) cc_final: 0.8712 (pt) REVERT: B 194 CYS cc_start: 0.7993 (m) cc_final: 0.7625 (m) REVERT: B 274 MET cc_start: 0.9021 (ptm) cc_final: 0.8039 (tmm) REVERT: B 293 TYR cc_start: 0.7391 (t80) cc_final: 0.6408 (t80) REVERT: B 298 LEU cc_start: 0.9324 (tt) cc_final: 0.8960 (pp) REVERT: B 433 GLU cc_start: 0.8073 (mp0) cc_final: 0.7540 (mp0) REVERT: B 498 MET cc_start: 0.7522 (tpp) cc_final: 0.7105 (tpp) REVERT: C 49 MET cc_start: 0.8543 (tpt) cc_final: 0.8175 (tpt) REVERT: C 105 LEU cc_start: 0.9315 (mp) cc_final: 0.9018 (mp) REVERT: C 114 LYS cc_start: 0.8551 (tptp) cc_final: 0.8304 (tptp) REVERT: C 115 PRO cc_start: 0.8478 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: C 172 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6517 (mtt180) REVERT: C 219 MET cc_start: 0.7959 (ptt) cc_final: 0.7666 (ptm) REVERT: C 251 MET cc_start: 0.7508 (tmm) cc_final: 0.6994 (tmm) REVERT: C 273 GLN cc_start: 0.8544 (tt0) cc_final: 0.7810 (tt0) REVERT: C 274 MET cc_start: 0.7925 (mmm) cc_final: 0.7377 (mmm) REVERT: C 314 MET cc_start: 0.8093 (tpt) cc_final: 0.7841 (tpp) REVERT: C 385 LEU cc_start: 0.8610 (mt) cc_final: 0.8330 (mt) REVERT: C 484 GLU cc_start: 0.8087 (tp30) cc_final: 0.7808 (tp30) REVERT: D 63 CYS cc_start: 0.8496 (m) cc_final: 0.7800 (m) REVERT: D 64 GLU cc_start: 0.7517 (pm20) cc_final: 0.7171 (mp0) REVERT: D 236 TYR cc_start: 0.4831 (t80) cc_final: 0.4448 (t80) REVERT: D 239 MET cc_start: 0.8327 (mmm) cc_final: 0.8000 (mmt) REVERT: D 247 MET cc_start: 0.8276 (ttp) cc_final: 0.7837 (ttp) REVERT: D 292 MET cc_start: 0.7987 (ttm) cc_final: 0.7501 (ttm) REVERT: D 342 THR cc_start: 0.7860 (p) cc_final: 0.7588 (p) REVERT: D 366 ASP cc_start: 0.8072 (t0) cc_final: 0.6879 (t0) REVERT: D 453 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 22 ARG cc_start: 0.7506 (mmp80) cc_final: 0.7076 (mmp80) REVERT: E 64 GLU cc_start: 0.6851 (pm20) cc_final: 0.6500 (pm20) REVERT: E 79 MET cc_start: 0.7558 (mpp) cc_final: 0.7245 (mpp) REVERT: E 80 SER cc_start: 0.9098 (m) cc_final: 0.8606 (t) REVERT: E 398 TYR cc_start: 0.8126 (t80) cc_final: 0.7899 (t80) REVERT: E 428 GLU cc_start: 0.8027 (pt0) cc_final: 0.7742 (pt0) REVERT: E 475 TYR cc_start: 0.8145 (t80) cc_final: 0.7833 (t80) REVERT: F 79 MET cc_start: 0.9001 (mmt) cc_final: 0.8622 (mmm) REVERT: F 184 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7823 (tt0) REVERT: F 239 MET cc_start: 0.6907 (ttm) cc_final: 0.6541 (ttm) REVERT: F 402 GLN cc_start: 0.8622 (tp40) cc_final: 0.8417 (tt0) REVERT: F 486 LYS cc_start: 0.9019 (tttp) cc_final: 0.8577 (tppp) REVERT: d 77 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7900 (mtp180) REVERT: d 104 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8275 (mtm180) REVERT: d 139 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8440 (mp10) REVERT: d 164 GLU cc_start: 0.7638 (mm-30) cc_final: 0.5821 (tp30) REVERT: d 205 LYS cc_start: 0.8214 (pttp) cc_final: 0.7884 (mmmt) REVERT: d 234 ASP cc_start: 0.7300 (p0) cc_final: 0.7009 (p0) REVERT: d 238 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7780 (mtmt) REVERT: g 73 ARG cc_start: 0.9003 (mmm160) cc_final: 0.8408 (mmm160) REVERT: g 121 MET cc_start: 0.6483 (ppp) cc_final: 0.4934 (ppp) REVERT: g 212 MET cc_start: 0.7971 (mtt) cc_final: 0.7551 (mtt) REVERT: g 303 GLN cc_start: 0.8589 (tp40) cc_final: 0.8319 (tp40) REVERT: g 310 GLU cc_start: 0.8804 (tp30) cc_final: 0.8321 (tp30) REVERT: g 354 LEU cc_start: 0.8475 (tt) cc_final: 0.8141 (pp) REVERT: e 11 ASN cc_start: 0.8627 (p0) cc_final: 0.8106 (p0) REVERT: e 19 VAL cc_start: 0.8085 (t) cc_final: 0.7868 (t) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1648 time to fit residues: 176.1595 Evaluate side-chains 502 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 194 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 236 GLN D 188 ASN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN d 141 HIS g 243 ASN g 301 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079411 restraints weight = 84890.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081647 restraints weight = 48657.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083186 restraints weight = 31666.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084118 restraints weight = 22562.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084898 restraints weight = 17623.820| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27514 Z= 0.143 Angle : 0.738 14.853 37329 Z= 0.366 Chirality : 0.047 0.298 4425 Planarity : 0.005 0.067 4851 Dihedral : 7.492 120.032 4002 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.41 (0.14), residues: 3544 helix: 0.31 (0.13), residues: 1501 sheet: -2.55 (0.23), residues: 470 loop : -1.59 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 418 TYR 0.026 0.002 TYR E 298 PHE 0.032 0.002 PHE B 390 TRP 0.007 0.001 TRP e 15 HIS 0.004 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00326 (27513) covalent geometry : angle 0.73809 (37327) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.98381 ( 2) hydrogen bonds : bond 0.03913 ( 1280) hydrogen bonds : angle 5.19989 ( 3714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.8582 (pt) cc_final: 0.8308 (pt) REVERT: A 157 MET cc_start: 0.7812 (ttm) cc_final: 0.7510 (ttm) REVERT: A 220 GLU cc_start: 0.8125 (pt0) cc_final: 0.7667 (pm20) REVERT: A 296 SER cc_start: 0.8442 (t) cc_final: 0.7267 (t) REVERT: A 300 GLU cc_start: 0.8309 (tt0) cc_final: 0.7878 (mt-10) REVERT: A 348 ASP cc_start: 0.8871 (p0) cc_final: 0.8547 (p0) REVERT: A 360 VAL cc_start: 0.7774 (m) cc_final: 0.7512 (m) REVERT: A 436 MET cc_start: 0.8885 (ppp) cc_final: 0.8609 (ppp) REVERT: A 484 GLU cc_start: 0.8456 (mp0) cc_final: 0.7773 (tm-30) REVERT: B 147 LEU cc_start: 0.8604 (tt) cc_final: 0.8099 (tt) REVERT: B 149 THR cc_start: 0.9405 (p) cc_final: 0.9111 (t) REVERT: B 194 CYS cc_start: 0.7923 (m) cc_final: 0.7539 (m) REVERT: B 274 MET cc_start: 0.8985 (ptm) cc_final: 0.8105 (tmm) REVERT: B 293 TYR cc_start: 0.7416 (t80) cc_final: 0.6306 (t80) REVERT: B 298 LEU cc_start: 0.9319 (tt) cc_final: 0.8945 (pp) REVERT: B 392 GLU cc_start: 0.7195 (pp20) cc_final: 0.6974 (pp20) REVERT: B 498 MET cc_start: 0.7521 (tpp) cc_final: 0.7094 (tpp) REVERT: C 49 MET cc_start: 0.8568 (tpt) cc_final: 0.8224 (tpt) REVERT: C 105 LEU cc_start: 0.9312 (mp) cc_final: 0.9036 (mp) REVERT: C 114 LYS cc_start: 0.8603 (tptp) cc_final: 0.8335 (tptp) REVERT: C 115 PRO cc_start: 0.8533 (Cg_exo) cc_final: 0.8221 (Cg_endo) REVERT: C 219 MET cc_start: 0.7913 (ptt) cc_final: 0.7631 (ptm) REVERT: C 251 MET cc_start: 0.7533 (tmm) cc_final: 0.7010 (tmm) REVERT: C 266 LYS cc_start: 0.8046 (mptt) cc_final: 0.7321 (mmmm) REVERT: C 273 GLN cc_start: 0.8527 (tt0) cc_final: 0.7799 (tt0) REVERT: C 274 MET cc_start: 0.7997 (mmm) cc_final: 0.7415 (mmm) REVERT: C 314 MET cc_start: 0.8074 (tpt) cc_final: 0.7380 (tpp) REVERT: C 385 LEU cc_start: 0.8647 (mt) cc_final: 0.8350 (mt) REVERT: C 484 GLU cc_start: 0.8070 (tp30) cc_final: 0.7750 (tp30) REVERT: C 491 LYS cc_start: 0.8560 (mttt) cc_final: 0.8091 (ptpt) REVERT: D 63 CYS cc_start: 0.8602 (m) cc_final: 0.8271 (m) REVERT: D 64 GLU cc_start: 0.7509 (pm20) cc_final: 0.7285 (pm20) REVERT: D 236 TYR cc_start: 0.4858 (t80) cc_final: 0.4602 (t80) REVERT: D 239 MET cc_start: 0.8317 (mmm) cc_final: 0.7928 (mmt) REVERT: D 247 MET cc_start: 0.8274 (ttp) cc_final: 0.7976 (ttp) REVERT: D 292 MET cc_start: 0.7980 (ttm) cc_final: 0.7431 (ttm) REVERT: D 342 THR cc_start: 0.7813 (p) cc_final: 0.7549 (p) REVERT: D 366 ASP cc_start: 0.8112 (t0) cc_final: 0.6924 (t0) REVERT: D 426 LYS cc_start: 0.8359 (mttm) cc_final: 0.7668 (ptpt) REVERT: D 453 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7822 (mm-30) REVERT: D 469 LEU cc_start: 0.8626 (mt) cc_final: 0.8367 (mt) REVERT: E 22 ARG cc_start: 0.7556 (mmp80) cc_final: 0.7113 (mmp80) REVERT: E 64 GLU cc_start: 0.6813 (pm20) cc_final: 0.6368 (pm20) REVERT: E 79 MET cc_start: 0.7598 (mpp) cc_final: 0.7167 (mpp) REVERT: E 80 SER cc_start: 0.9123 (m) cc_final: 0.8641 (t) REVERT: E 428 GLU cc_start: 0.8053 (pt0) cc_final: 0.7841 (pt0) REVERT: E 475 TYR cc_start: 0.8140 (t80) cc_final: 0.7780 (t80) REVERT: F 79 MET cc_start: 0.8972 (mmt) cc_final: 0.8646 (mmm) REVERT: F 184 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7839 (tt0) REVERT: F 239 MET cc_start: 0.6970 (ttm) cc_final: 0.6591 (ttm) REVERT: F 412 GLU cc_start: 0.5413 (tp30) cc_final: 0.5160 (tp30) REVERT: F 486 LYS cc_start: 0.9012 (tttp) cc_final: 0.8572 (tppp) REVERT: d 77 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7849 (mtp180) REVERT: d 104 ARG cc_start: 0.8654 (tpt170) cc_final: 0.8366 (mtm180) REVERT: d 139 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8472 (mp10) REVERT: d 164 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6029 (tp30) REVERT: d 205 LYS cc_start: 0.8111 (pttp) cc_final: 0.7804 (mmmt) REVERT: d 210 LYS cc_start: 0.8440 (tptt) cc_final: 0.7927 (mmtm) REVERT: d 238 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7666 (mtmt) REVERT: g 46 GLU cc_start: 0.8055 (mp0) cc_final: 0.6658 (pp20) REVERT: g 73 ARG cc_start: 0.9011 (mmm160) cc_final: 0.8453 (mmm160) REVERT: g 121 MET cc_start: 0.6501 (ppp) cc_final: 0.5042 (ppp) REVERT: g 212 MET cc_start: 0.7945 (mtt) cc_final: 0.7584 (mtt) REVERT: g 310 GLU cc_start: 0.8803 (tp30) cc_final: 0.8307 (tp30) REVERT: e 11 ASN cc_start: 0.8697 (p0) cc_final: 0.8178 (p0) REVERT: e 19 VAL cc_start: 0.8131 (t) cc_final: 0.7870 (t) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.1655 time to fit residues: 175.5654 Evaluate side-chains 514 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 252 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 191 optimal weight: 0.0070 chunk 244 optimal weight: 0.8980 chunk 176 optimal weight: 0.3980 chunk 264 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS B 186 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN D 188 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080107 restraints weight = 84522.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082351 restraints weight = 48873.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083864 restraints weight = 31809.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084920 restraints weight = 22731.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.085601 restraints weight = 17479.666| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27514 Z= 0.138 Angle : 0.739 14.752 37329 Z= 0.366 Chirality : 0.047 0.309 4425 Planarity : 0.005 0.067 4851 Dihedral : 7.371 121.913 4002 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.35 (0.14), residues: 3544 helix: 0.33 (0.13), residues: 1491 sheet: -2.46 (0.24), residues: 457 loop : -1.55 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 418 TYR 0.024 0.002 TYR E 385 PHE 0.030 0.002 PHE B 390 TRP 0.008 0.001 TRP e 15 HIS 0.004 0.001 HIS F 133 Details of bonding type rmsd covalent geometry : bond 0.00313 (27513) covalent geometry : angle 0.73944 (37327) SS BOND : bond 0.00160 ( 1) SS BOND : angle 0.97584 ( 2) hydrogen bonds : bond 0.03899 ( 1280) hydrogen bonds : angle 5.18696 ( 3714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4589.10 seconds wall clock time: 80 minutes 13.14 seconds (4813.14 seconds total)