Starting phenix.real_space_refine on Mon Sep 14 02:15:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vog_21263/09_2026/6vog_21263.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vog_21263/09_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_21263/09_2026/6vog_21263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vog_21263/09_2026/6vog_21263.map" model { file = "/net/cci-nas-00/data/ceres_data/6vog_21263/09_2026/6vog_21263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vog_21263/09_2026/6vog_21263.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vog_21263/09_2026/6vog_21263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vog_21263/09_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-2.2.1-6174/lib/python3.11/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: 5.81, 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: 2.37 Conformation dependent library (CDL) restraints added in 996.8 milliseconds 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: 0.84 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: 5.41 Time building geometry restraints manager: 3.05 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: 15519 23.61 - 47.22: 1107 47.22 - 70.84: 124 70.84 - 94.45: 41 94.45 - 118.06: 3 Dihedral angle restraints: 16794 sinusoidal: 6594 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 16791 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.950 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 16.245 118.062 10245 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/Z covalent geometry : bond 0.00662 / 0.35 (27513) covalent geometry : angle 1.07846 / 0.66 (37327) SS BOND : bond 0.00477 / 0.25 ( 1) SS BOND : angle 1.69738 / 0.98 ( 2) hydrogen bonds : bond 0.14607 / 10.21 ( 1280) hydrogen bonds : angle 7.38149 / 5.14 ( 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 : 1.071 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: 0.1919 time to fit residues: 288.6715 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 : 1.137 ------------------------------------------------------------------------------- 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... 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 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078430 restraints weight = 85260.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080701 restraints weight = 47407.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.082226 restraints weight = 30022.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083241 restraints weight = 20934.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083895 restraints weight = 15943.402| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2631 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= 0.161 Angle : 0.725 11.605 37329 Z= 0.373 Chirality : 0.046 0.274 4425 Planarity : 0.006 0.066 4851 Dihedral : 7.598 118.071 3878 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % 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: -2.79 (0.13), residues: 3544 helix: -0.88 (0.12), residues: 1486 sheet: -3.39 (0.19), residues: 487 loop : -2.19 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 144 TYR 0.027 0.002 TYR A 221 PHE 0.033 0.002 PHE F 343 TRP 0.010 0.002 TRP e 15 HIS 0.009 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (27513) covalent geometry : angle 0.72483 / 0.37 (37327) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 1.00046 / 0.58 ( 2) hydrogen bonds : bond 0.04515 / 3.06 ( 1280) hydrogen bonds : angle 5.96242 / 4.07 ( 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 817 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 813 time to evaluate : 1.061 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: 0.8933 (pt) cc_final: 0.8172 (pt) REVERT: A 199 ILE cc_start: 0.9093 (mt) cc_final: 0.8857 (mt) REVERT: A 230 ASP cc_start: 0.7419 (p0) cc_final: 0.6815 (p0) REVERT: A 263 ASP cc_start: 0.7758 (t0) cc_final: 0.7512 (t0) REVERT: A 287 TYR cc_start: 0.7595 (m-80) cc_final: 0.7234 (m-80) REVERT: A 292 PHE cc_start: 0.8055 (t80) cc_final: 0.7638 (t80) REVERT: A 300 GLU cc_start: 0.8838 (tt0) cc_final: 0.8250 (mt-10) REVERT: A 333 THR cc_start: 0.9086 (t) cc_final: 0.8788 (t) REVERT: A 348 ASP cc_start: 0.8395 (p0) cc_final: 0.8118 (p0) REVERT: A 436 MET cc_start: 0.8785 (ppp) cc_final: 0.8358 (ppp) REVERT: A 498 MET cc_start: 0.7951 (mmm) cc_final: 0.7357 (tpt) REVERT: B 14 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8107 (ttp-110) REVERT: B 157 MET cc_start: 0.7768 (mmm) cc_final: 0.7249 (tpp) REVERT: B 171 ASP cc_start: 0.6982 (t0) cc_final: 0.6650 (m-30) REVERT: B 194 CYS cc_start: 0.8146 (m) cc_final: 0.7810 (m) REVERT: B 274 MET cc_start: 0.8847 (ptm) cc_final: 0.8089 (tmm) REVERT: B 293 TYR cc_start: 0.7253 (t80) cc_final: 0.6111 (t80) REVERT: B 386 GLU cc_start: 0.7163 (tp30) cc_final: 0.6915 (tm-30) REVERT: B 457 TYR cc_start: 0.8963 (t80) cc_final: 0.8658 (t80) REVERT: B 498 MET cc_start: 0.7888 (ttm) cc_final: 0.7597 (mtt) REVERT: C 14 ARG cc_start: 0.5819 (mmt90) cc_final: 0.5091 (mpt180) REVERT: C 15 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7331 (mm-30) REVERT: C 108 VAL cc_start: 0.9090 (t) cc_final: 0.8827 (t) REVERT: C 165 ARG cc_start: 0.6203 (ptp90) cc_final: 0.5971 (ptp90) REVERT: C 251 MET cc_start: 0.7526 (ttp) cc_final: 0.6910 (ttp) REVERT: C 273 GLN cc_start: 0.8596 (tt0) cc_final: 0.7686 (tt0) REVERT: C 274 MET cc_start: 0.7952 (mmm) cc_final: 0.7685 (mmm) REVERT: C 293 TYR cc_start: 0.8872 (t80) cc_final: 0.8629 (t80) REVERT: C 295 HIS cc_start: 0.8534 (m170) cc_final: 0.8212 (m170) REVERT: C 385 LEU cc_start: 0.8513 (mt) cc_final: 0.8074 (mt) REVERT: C 433 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6302 (tp30) REVERT: C 462 ARG cc_start: 0.8195 (ptm-80) cc_final: 0.7737 (ptm-80) REVERT: D 205 ARG cc_start: 0.6335 (mpt-90) cc_final: 0.6127 (mpt-90) REVERT: D 239 MET cc_start: 0.8323 (mmm) cc_final: 0.8090 (mmm) REVERT: D 247 MET cc_start: 0.8557 (ttp) cc_final: 0.8050 (ttp) REVERT: D 292 MET cc_start: 0.7929 (ttm) cc_final: 0.7635 (ttm) REVERT: D 311 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7700 (tm-30) REVERT: D 335 THR cc_start: 0.8826 (t) cc_final: 0.8555 (m) REVERT: D 345 HIS cc_start: 0.6725 (t70) cc_final: 0.6373 (t70) REVERT: D 453 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 461 ILE cc_start: 0.8234 (mt) cc_final: 0.7976 (mt) REVERT: E 79 MET cc_start: 0.7846 (mpp) cc_final: 0.7249 (mpp) REVERT: E 128 THR cc_start: 0.7832 (p) cc_final: 0.7485 (p) REVERT: E 251 LEU cc_start: 0.8104 (tp) cc_final: 0.7659 (tp) REVERT: E 264 ASN cc_start: 0.8005 (m110) cc_final: 0.7319 (t0) REVERT: E 279 VAL cc_start: 0.9153 (t) cc_final: 0.8938 (t) REVERT: E 375 LEU cc_start: 0.9154 (tp) cc_final: 0.8830 (tp) REVERT: F 79 MET cc_start: 0.8808 (mmt) cc_final: 0.8295 (mmm) REVERT: F 145 LYS cc_start: 0.8275 (tptp) cc_final: 0.7733 (pttm) REVERT: F 168 ILE cc_start: 0.7853 (mm) cc_final: 0.7438 (mt) REVERT: F 184 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7815 (tp30) REVERT: F 214 MET cc_start: 0.7171 (mmp) cc_final: 0.6870 (tmm) REVERT: F 239 MET cc_start: 0.7201 (ttm) cc_final: 0.6898 (ttm) REVERT: F 325 GLN cc_start: 0.7153 (pm20) cc_final: 0.6892 (pm20) REVERT: F 393 GLU cc_start: 0.7677 (mp0) cc_final: 0.7387 (mp0) REVERT: F 412 GLU cc_start: 0.4933 (mm-30) cc_final: 0.4384 (tp30) REVERT: F 481 ASP cc_start: 0.7800 (m-30) cc_final: 0.7565 (m-30) REVERT: F 486 LYS cc_start: 0.8982 (tttp) cc_final: 0.8514 (tppp) REVERT: d 98 ASP cc_start: 0.8647 (t0) cc_final: 0.8421 (t0) REVERT: d 104 ARG cc_start: 0.8589 (tpt170) cc_final: 0.8319 (mtm180) REVERT: d 114 PHE cc_start: 0.8552 (t80) cc_final: 0.8306 (t80) REVERT: d 125 LYS cc_start: 0.8401 (mtpt) cc_final: 0.7949 (mttp) REVERT: d 139 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8205 (mp10) REVERT: d 151 ASP cc_start: 0.8161 (m-30) cc_final: 0.7940 (m-30) REVERT: d 164 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6953 (tp30) REVERT: d 193 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8471 (tt0) REVERT: g 81 ASN cc_start: 0.8250 (t0) cc_final: 0.7972 (t0) REVERT: g 189 LYS cc_start: 0.8632 (mttp) cc_final: 0.8378 (mmmt) REVERT: g 260 LYS cc_start: 0.7900 (pttm) cc_final: 0.7339 (pttm) REVERT: e 11 ASN cc_start: 0.8447 (p0) cc_final: 0.7565 (p0) REVERT: e 18 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7925 (mt-10) REVERT: e 19 VAL cc_start: 0.7938 (t) cc_final: 0.7417 (t) REVERT: e 117 LEU cc_start: 0.8510 (pp) cc_final: 0.7972 (pp) REVERT: e 124 THR cc_start: 0.7985 (m) cc_final: 0.7462 (m) outliers start: 4 outliers final: 0 residues processed: 816 average time/residue: 0.1821 time to fit residues: 236.3692 Evaluate side-chains 545 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 291 optimal weight: 0.9980 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN B 497 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN F 472 GLN g 134 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 56 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.078119 restraints weight = 85001.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080396 restraints weight = 47535.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081944 restraints weight = 30203.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082982 restraints weight = 21046.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083705 restraints weight = 16038.645| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27514 Z= 0.152 Angle : 0.711 11.398 37329 Z= 0.360 Chirality : 0.046 0.264 4425 Planarity : 0.005 0.067 4851 Dihedral : 7.281 120.522 3878 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % 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: -2.25 (0.13), residues: 3544 helix: -0.31 (0.13), residues: 1470 sheet: -3.32 (0.20), residues: 462 loop : -1.99 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 291 TYR 0.021 0.002 TYR B 271 PHE 0.025 0.002 PHE F 276 TRP 0.015 0.002 TRP e 15 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (27513) covalent geometry : angle 0.71103 / 0.36 (37327) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 1.52929 / 0.90 ( 2) hydrogen bonds : bond 0.04243 / 2.88 ( 1280) hydrogen bonds : angle 5.63095 / 3.84 ( 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 759 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 757 time to evaluate : 1.170 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: A 61 ILE cc_start: 0.8940 (pt) cc_final: 0.8124 (pt) REVERT: A 63 ILE cc_start: 0.9525 (mm) cc_final: 0.8993 (mm) REVERT: A 137 ILE cc_start: 0.7173 (mp) cc_final: 0.6963 (mp) REVERT: A 155 ASP cc_start: 0.7710 (m-30) cc_final: 0.7294 (m-30) REVERT: A 287 TYR cc_start: 0.7593 (m-80) cc_final: 0.7300 (m-10) REVERT: A 300 GLU cc_start: 0.8888 (tt0) cc_final: 0.7852 (mt-10) REVERT: A 348 ASP cc_start: 0.8696 (p0) cc_final: 0.8322 (p0) REVERT: A 436 MET cc_start: 0.8912 (ppp) cc_final: 0.8371 (ppp) REVERT: A 498 MET cc_start: 0.7818 (mmm) cc_final: 0.7300 (tpt) REVERT: B 14 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8121 (ttp-110) REVERT: B 194 CYS cc_start: 0.8120 (m) cc_final: 0.7646 (m) REVERT: B 274 MET cc_start: 0.8876 (ptm) cc_final: 0.8117 (tmm) REVERT: B 293 TYR cc_start: 0.7295 (t80) cc_final: 0.6247 (t80) REVERT: B 348 ASP cc_start: 0.6376 (t0) cc_final: 0.6096 (t0) REVERT: B 386 GLU cc_start: 0.7143 (tp30) cc_final: 0.6829 (tm-30) REVERT: B 482 PHE cc_start: 0.7514 (p90) cc_final: 0.7207 (p90) REVERT: C 14 ARG cc_start: 0.5699 (mmt90) cc_final: 0.4994 (mmt180) REVERT: C 15 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7306 (mm-30) REVERT: C 45 LEU cc_start: 0.8470 (tp) cc_final: 0.8016 (tt) REVERT: C 49 MET cc_start: 0.8248 (tpt) cc_final: 0.7180 (tpt) REVERT: C 105 LEU cc_start: 0.9322 (mp) cc_final: 0.9080 (mp) REVERT: C 165 ARG cc_start: 0.5458 (ptp90) cc_final: 0.4891 (ptp-170) REVERT: C 251 MET cc_start: 0.7522 (ttp) cc_final: 0.6890 (ttp) REVERT: C 274 MET cc_start: 0.8011 (mmm) cc_final: 0.7595 (mmm) REVERT: C 293 TYR cc_start: 0.8947 (t80) cc_final: 0.8574 (t80) REVERT: C 295 HIS cc_start: 0.8391 (m170) cc_final: 0.8160 (m170) REVERT: C 385 LEU cc_start: 0.8501 (mt) cc_final: 0.8127 (mt) REVERT: C 462 ARG cc_start: 0.8078 (ptm-80) cc_final: 0.7816 (ptm-80) REVERT: D 27 ILE cc_start: 0.9036 (pt) cc_final: 0.8784 (pt) REVERT: D 182 ILE cc_start: 0.8751 (mm) cc_final: 0.8063 (mm) REVERT: D 236 TYR cc_start: 0.4825 (t80) cc_final: 0.4266 (t80) REVERT: D 239 MET cc_start: 0.8320 (mmm) cc_final: 0.7901 (mmm) REVERT: D 247 MET cc_start: 0.8289 (ttp) cc_final: 0.7976 (ttp) REVERT: D 285 VAL cc_start: 0.9382 (t) cc_final: 0.9162 (t) REVERT: D 305 GLU cc_start: 0.6760 (tt0) cc_final: 0.6515 (tt0) REVERT: D 335 THR cc_start: 0.8773 (t) cc_final: 0.8497 (m) REVERT: D 345 HIS cc_start: 0.6630 (t70) cc_final: 0.5645 (t70) REVERT: D 413 LEU cc_start: 0.8063 (mp) cc_final: 0.7776 (mp) REVERT: D 453 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 469 LEU cc_start: 0.8578 (mt) cc_final: 0.7860 (mt) REVERT: E 64 GLU cc_start: 0.7160 (pm20) cc_final: 0.6907 (pm20) REVERT: E 79 MET cc_start: 0.7945 (mpp) cc_final: 0.7662 (mpp) REVERT: E 128 THR cc_start: 0.7826 (p) cc_final: 0.7066 (p) REVERT: E 183 MET cc_start: 0.8982 (mtt) cc_final: 0.8775 (mtp) REVERT: E 248 ARG cc_start: 0.7016 (mmt180) cc_final: 0.6810 (mmt180) REVERT: E 251 LEU cc_start: 0.8319 (tp) cc_final: 0.7983 (tp) REVERT: E 264 ASN cc_start: 0.8009 (m110) cc_final: 0.7654 (m110) REVERT: E 305 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7257 (mm-30) REVERT: E 375 LEU cc_start: 0.8996 (tp) cc_final: 0.8785 (tp) REVERT: E 396 GLN cc_start: 0.8962 (tp40) cc_final: 0.8267 (tp40) REVERT: E 488 MET cc_start: 0.8098 (tmm) cc_final: 0.7747 (tmm) REVERT: F 145 LYS cc_start: 0.8366 (tptp) cc_final: 0.7949 (pttm) REVERT: F 239 MET cc_start: 0.7071 (ttm) cc_final: 0.6483 (ttm) REVERT: F 273 ASP cc_start: 0.7854 (p0) cc_final: 0.7510 (p0) REVERT: F 311 GLU cc_start: 0.7986 (tp30) cc_final: 0.7525 (tp30) REVERT: F 325 GLN cc_start: 0.7220 (pm20) cc_final: 0.6231 (pm20) REVERT: F 346 LEU cc_start: 0.8994 (pp) cc_final: 0.8649 (mt) REVERT: F 412 GLU cc_start: 0.4977 (mm-30) cc_final: 0.4489 (tp30) REVERT: F 481 ASP cc_start: 0.7855 (m-30) cc_final: 0.7549 (m-30) REVERT: F 486 LYS cc_start: 0.8989 (tttp) cc_final: 0.8521 (tppp) REVERT: d 104 ARG cc_start: 0.8586 (tpt170) cc_final: 0.8315 (mtm180) REVERT: d 125 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8071 (mttp) REVERT: d 139 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8592 (mp10) REVERT: d 151 ASP cc_start: 0.7840 (m-30) cc_final: 0.7537 (m-30) REVERT: d 164 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6617 (tp30) REVERT: d 193 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8423 (tt0) REVERT: g 64 MET cc_start: 0.8220 (tpp) cc_final: 0.7853 (tpp) REVERT: g 81 ASN cc_start: 0.8133 (t0) cc_final: 0.7913 (t0) REVERT: g 180 PHE cc_start: 0.6793 (t80) cc_final: 0.6568 (t80) REVERT: g 189 LYS cc_start: 0.8759 (mttp) cc_final: 0.8449 (mmmt) REVERT: g 287 ASP cc_start: 0.7510 (m-30) cc_final: 0.7287 (m-30) REVERT: g 302 SER cc_start: 0.9199 (t) cc_final: 0.8991 (t) REVERT: g 303 GLN cc_start: 0.8562 (tp40) cc_final: 0.8195 (tp40) REVERT: g 310 GLU cc_start: 0.8539 (tt0) cc_final: 0.7957 (tp30) REVERT: g 315 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7213 (mm-30) REVERT: e 11 ASN cc_start: 0.8563 (p0) cc_final: 0.7798 (p0) REVERT: e 19 VAL cc_start: 0.8090 (t) cc_final: 0.7728 (t) REVERT: e 117 LEU cc_start: 0.8542 (pp) cc_final: 0.8236 (pp) outliers start: 2 outliers final: 0 residues processed: 757 average time/residue: 0.1826 time to fit residues: 221.4393 Evaluate side-chains 541 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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: 6.9990 chunk 212 optimal weight: 0.8980 chunk 345 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 334 ASN B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 201 GLN C 236 GLN C 473 GLN D 25 GLN ** D 274 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 d 247 GLN g 76 GLN g 184 ASN g 243 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 56 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075319 restraints weight = 85844.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.077531 restraints weight = 48227.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079029 restraints weight = 30924.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080053 restraints weight = 21799.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080714 restraints weight = 16684.490| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27514 Z= 0.195 Angle : 0.731 12.089 37329 Z= 0.371 Chirality : 0.047 0.242 4425 Planarity : 0.005 0.063 4851 Dihedral : 7.203 122.088 3878 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.83 % 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: -2.06 (0.14), residues: 3544 helix: -0.15 (0.13), residues: 1486 sheet: -3.22 (0.20), residues: 492 loop : -1.86 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 462 TYR 0.029 0.002 TYR C 439 PHE 0.033 0.002 PHE A 292 TRP 0.010 0.002 TRP e 15 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (27513) covalent geometry : angle 0.73119 / 0.37 (37327) SS BOND : bond 0.02124 / 1.12 ( 1) SS BOND : angle 1.01784 / 0.54 ( 2) hydrogen bonds : bond 0.04314 / 2.92 ( 1280) hydrogen bonds : angle 5.53764 / 3.78 ( 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 704 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 703 time to evaluate : 0.992 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 77 MET cc_start: 0.7611 (mtm) cc_final: 0.7336 (mtp) REVERT: A 138 MET cc_start: 0.7190 (tpp) cc_final: 0.6773 (tpp) REVERT: A 157 MET cc_start: 0.7951 (ttm) cc_final: 0.7738 (ttm) REVERT: A 287 TYR cc_start: 0.7762 (m-80) cc_final: 0.7391 (m-10) REVERT: A 300 GLU cc_start: 0.8990 (tt0) cc_final: 0.7577 (mt-10) REVERT: A 348 ASP cc_start: 0.8601 (p0) cc_final: 0.8203 (p0) REVERT: A 349 LEU cc_start: 0.9355 (mt) cc_final: 0.9083 (mt) REVERT: A 436 MET cc_start: 0.8852 (ppp) cc_final: 0.8463 (ppp) REVERT: A 484 GLU cc_start: 0.8441 (mp0) cc_final: 0.7942 (tm-30) REVERT: A 498 MET cc_start: 0.7960 (mmm) cc_final: 0.7452 (tpt) REVERT: B 194 CYS cc_start: 0.8181 (m) cc_final: 0.7772 (m) REVERT: B 274 MET cc_start: 0.8908 (ptm) cc_final: 0.8048 (tmm) REVERT: B 293 TYR cc_start: 0.7532 (t80) cc_final: 0.6477 (t80) REVERT: B 348 ASP cc_start: 0.6253 (t0) cc_final: 0.5684 (t0) REVERT: B 482 PHE cc_start: 0.7685 (p90) cc_final: 0.7326 (p90) REVERT: B 498 MET cc_start: 0.7433 (mtt) cc_final: 0.7076 (tpp) REVERT: C 15 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7359 (mm-30) REVERT: C 49 MET cc_start: 0.7709 (tpt) cc_final: 0.7459 (tpt) REVERT: C 259 ILE cc_start: 0.8873 (pt) cc_final: 0.8563 (pt) REVERT: C 262 ASP cc_start: 0.7480 (p0) cc_final: 0.7262 (p0) REVERT: C 273 GLN cc_start: 0.8696 (tt0) cc_final: 0.7603 (tt0) REVERT: C 293 TYR cc_start: 0.8964 (t80) cc_final: 0.8623 (t80) REVERT: D 40 MET cc_start: 0.8183 (mmm) cc_final: 0.7923 (mmm) REVERT: D 63 CYS cc_start: 0.8245 (m) cc_final: 0.7866 (m) REVERT: D 182 ILE cc_start: 0.8990 (mm) cc_final: 0.8610 (mm) REVERT: D 236 TYR cc_start: 0.4617 (t80) cc_final: 0.4136 (t80) REVERT: D 239 MET cc_start: 0.8364 (mmm) cc_final: 0.8004 (mmm) REVERT: D 272 ILE cc_start: 0.8705 (tt) cc_final: 0.8394 (mt) REVERT: D 292 MET cc_start: 0.7951 (ttm) cc_final: 0.7403 (ttm) REVERT: D 335 THR cc_start: 0.8869 (t) cc_final: 0.8598 (m) REVERT: D 345 HIS cc_start: 0.6779 (t70) cc_final: 0.6216 (t70) REVERT: D 453 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 79 MET cc_start: 0.8013 (mpp) cc_final: 0.7762 (mpp) REVERT: E 183 MET cc_start: 0.9061 (mtt) cc_final: 0.8851 (mtp) REVERT: E 251 LEU cc_start: 0.8346 (tp) cc_final: 0.7931 (tp) REVERT: E 299 GLN cc_start: 0.8561 (pm20) cc_final: 0.7858 (pm20) REVERT: E 375 LEU cc_start: 0.8996 (tp) cc_final: 0.8759 (tp) REVERT: E 393 GLU cc_start: 0.7958 (tt0) cc_final: 0.7649 (tp30) REVERT: E 396 GLN cc_start: 0.8999 (tp40) cc_final: 0.8353 (tp40) REVERT: E 429 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7635 (mtm-85) REVERT: E 488 MET cc_start: 0.8139 (tmm) cc_final: 0.7922 (tmm) REVERT: F 239 MET cc_start: 0.7268 (ttm) cc_final: 0.6526 (ttm) REVERT: F 273 ASP cc_start: 0.8116 (p0) cc_final: 0.7714 (p0) REVERT: F 346 LEU cc_start: 0.9074 (pp) cc_final: 0.8699 (mt) REVERT: F 374 MET cc_start: 0.8643 (mmt) cc_final: 0.8438 (mpp) REVERT: F 412 GLU cc_start: 0.5297 (mm-30) cc_final: 0.4837 (tp30) REVERT: F 481 ASP cc_start: 0.8013 (m-30) cc_final: 0.7690 (m-30) REVERT: F 486 LYS cc_start: 0.8982 (tttp) cc_final: 0.8540 (tppp) REVERT: d 77 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7946 (mtp180) REVERT: d 98 ASP cc_start: 0.8491 (t0) cc_final: 0.8283 (t0) REVERT: d 112 TYR cc_start: 0.7884 (t80) cc_final: 0.7496 (t80) REVERT: d 114 PHE cc_start: 0.8775 (t80) cc_final: 0.8541 (t80) REVERT: d 125 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8049 (mttp) REVERT: d 139 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8474 (mp10) REVERT: d 164 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7243 (tp30) REVERT: d 193 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8484 (tt0) REVERT: g 180 PHE cc_start: 0.7010 (t80) cc_final: 0.6742 (t80) REVERT: g 189 LYS cc_start: 0.8827 (mttp) cc_final: 0.8455 (mmmt) REVERT: g 354 LEU cc_start: 0.8474 (tt) cc_final: 0.8208 (pp) REVERT: e 11 ASN cc_start: 0.8622 (p0) cc_final: 0.8008 (p0) REVERT: e 19 VAL cc_start: 0.8066 (t) cc_final: 0.7728 (t) REVERT: e 124 THR cc_start: 0.7735 (m) cc_final: 0.7286 (m) outliers start: 1 outliers final: 0 residues processed: 704 average time/residue: 0.1765 time to fit residues: 199.7077 Evaluate side-chains 485 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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: 5.9990 chunk 234 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 266 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 212 ASN B 186 ASN B 342 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 497 GLN ** D 274 ASN ** 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 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** 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 472 GLN ** 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 = 0.3396 r_free = 0.3396 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076333 restraints weight = 84990.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078536 restraints weight = 47830.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080039 restraints weight = 30724.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081055 restraints weight = 21633.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081703 restraints weight = 16592.308| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27514 Z= 0.157 Angle : 0.717 12.599 37329 Z= 0.360 Chirality : 0.047 0.253 4425 Planarity : 0.005 0.064 4851 Dihedral : 7.076 125.439 3878 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % 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: -1.78 (0.14), residues: 3544 helix: 0.13 (0.13), residues: 1477 sheet: -3.09 (0.21), residues: 484 loop : -1.76 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 280 TYR 0.023 0.002 TYR E 298 PHE 0.029 0.002 PHE A 292 TRP 0.009 0.002 TRP e 15 HIS 0.005 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (27513) covalent geometry : angle 0.71715 / 0.36 (37327) SS BOND : bond 0.01969 / 1.04 ( 1) SS BOND : angle 1.72619 / 0.99 ( 2) hydrogen bonds : bond 0.04120 / 2.79 ( 1280) hydrogen bonds : angle 5.39275 / 3.69 ( 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 687 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 686 time to evaluate : 1.071 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: A 77 MET cc_start: 0.7691 (mtm) cc_final: 0.7347 (mtp) REVERT: A 157 MET cc_start: 0.7791 (ttm) cc_final: 0.7486 (ttm) REVERT: A 230 ASP cc_start: 0.7623 (p0) cc_final: 0.7419 (p0) REVERT: A 287 TYR cc_start: 0.7672 (m-80) cc_final: 0.7324 (m-10) REVERT: A 300 GLU cc_start: 0.8831 (tt0) cc_final: 0.7744 (mt-10) REVERT: A 348 ASP cc_start: 0.8703 (p0) cc_final: 0.8415 (p0) REVERT: A 436 MET cc_start: 0.8773 (ppp) cc_final: 0.8354 (ppp) REVERT: A 484 GLU cc_start: 0.8478 (mp0) cc_final: 0.7876 (tm-30) REVERT: A 498 MET cc_start: 0.8339 (tpt) cc_final: 0.7585 (tpt) REVERT: B 194 CYS cc_start: 0.8269 (m) cc_final: 0.7843 (m) REVERT: B 274 MET cc_start: 0.8961 (ptm) cc_final: 0.8055 (tmm) REVERT: B 293 TYR cc_start: 0.7415 (t80) cc_final: 0.6373 (t80) REVERT: B 482 PHE cc_start: 0.7633 (p90) cc_final: 0.7248 (p90) REVERT: C 15 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7337 (mm-30) REVERT: C 49 MET cc_start: 0.7745 (tpt) cc_final: 0.7463 (tpt) REVERT: C 82 MET cc_start: 0.7264 (pmm) cc_final: 0.6990 (pmm) REVERT: C 105 LEU cc_start: 0.9355 (mp) cc_final: 0.9083 (mp) REVERT: C 165 ARG cc_start: 0.5729 (ptp-170) cc_final: 0.4917 (ptp-170) REVERT: C 251 MET cc_start: 0.7546 (ttp) cc_final: 0.7190 (ttp) REVERT: C 266 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7956 (mmtt) REVERT: C 274 MET cc_start: 0.7904 (mmm) cc_final: 0.7498 (mmm) REVERT: C 293 TYR cc_start: 0.8960 (t80) cc_final: 0.8649 (t80) REVERT: C 314 MET cc_start: 0.8591 (tpt) cc_final: 0.7959 (tpp) REVERT: C 385 LEU cc_start: 0.8586 (mt) cc_final: 0.8201 (mt) REVERT: D 63 CYS cc_start: 0.8228 (m) cc_final: 0.7960 (m) REVERT: D 182 ILE cc_start: 0.9178 (mm) cc_final: 0.8845 (mm) REVERT: D 236 TYR cc_start: 0.4732 (t80) cc_final: 0.4241 (t80) REVERT: D 239 MET cc_start: 0.8366 (mmm) cc_final: 0.7917 (mmt) REVERT: D 292 MET cc_start: 0.8020 (ttm) cc_final: 0.7451 (ttm) REVERT: D 335 THR cc_start: 0.8841 (t) cc_final: 0.8537 (m) REVERT: D 426 LYS cc_start: 0.8359 (mttm) cc_final: 0.7654 (ptpt) REVERT: D 453 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7802 (mm-30) REVERT: E 22 ARG cc_start: 0.7423 (mmp80) cc_final: 0.7158 (mmp80) REVERT: E 64 GLU cc_start: 0.7065 (pm20) cc_final: 0.6503 (pm20) REVERT: E 183 MET cc_start: 0.9051 (mtt) cc_final: 0.8835 (mtp) REVERT: E 248 ARG cc_start: 0.6938 (mmt180) cc_final: 0.6598 (mmt180) REVERT: E 299 GLN cc_start: 0.8345 (pm20) cc_final: 0.7705 (pm20) REVERT: E 375 LEU cc_start: 0.9058 (tp) cc_final: 0.8843 (tp) REVERT: E 393 GLU cc_start: 0.7945 (tt0) cc_final: 0.7662 (tp30) REVERT: E 396 GLN cc_start: 0.9017 (tp40) cc_final: 0.8453 (tp40) REVERT: E 475 TYR cc_start: 0.8048 (t80) cc_final: 0.7840 (t80) REVERT: F 79 MET cc_start: 0.8823 (mmt) cc_final: 0.8442 (mmm) REVERT: F 85 LEU cc_start: 0.9516 (pt) cc_final: 0.9302 (pp) REVERT: F 213 TYR cc_start: 0.8484 (t80) cc_final: 0.7990 (t80) REVERT: F 247 MET cc_start: 0.8002 (tpp) cc_final: 0.7651 (tpt) REVERT: F 412 GLU cc_start: 0.5411 (mm-30) cc_final: 0.5020 (tp30) REVERT: F 475 TYR cc_start: 0.7512 (t80) cc_final: 0.7093 (t80) REVERT: F 481 ASP cc_start: 0.8055 (m-30) cc_final: 0.7779 (m-30) REVERT: F 486 LYS cc_start: 0.9010 (tttp) cc_final: 0.8527 (tppp) REVERT: d 77 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7875 (mtp180) REVERT: d 104 ARG cc_start: 0.8593 (tpt170) cc_final: 0.8247 (mtm180) REVERT: d 112 TYR cc_start: 0.7804 (t80) cc_final: 0.7600 (t80) REVERT: d 125 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8121 (mttp) REVERT: d 149 LEU cc_start: 0.9017 (mm) cc_final: 0.8508 (tp) REVERT: d 164 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6676 (tp30) REVERT: d 193 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8478 (tt0) REVERT: g 46 GLU cc_start: 0.7566 (mp0) cc_final: 0.6540 (pp20) REVERT: g 189 LYS cc_start: 0.8846 (mttp) cc_final: 0.8524 (mmmt) REVERT: g 303 GLN cc_start: 0.8553 (tp40) cc_final: 0.8185 (tp40) REVERT: g 320 MET cc_start: 0.7848 (mmm) cc_final: 0.6257 (tmm) REVERT: g 354 LEU cc_start: 0.8413 (tt) cc_final: 0.8164 (pp) REVERT: e 19 VAL cc_start: 0.8077 (t) cc_final: 0.7761 (t) outliers start: 1 outliers final: 0 residues processed: 686 average time/residue: 0.1774 time to fit residues: 196.8953 Evaluate side-chains 493 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 4.9990 chunk 204 optimal weight: 0.0870 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 0.4980 chunk 214 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 0.0030 overall best weight: 1.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN B 186 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 495 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 240 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 299 GLN g 290 GLN g 301 ASN g 309 GLN e 56 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076075 restraints weight = 85721.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078318 restraints weight = 48435.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079821 restraints weight = 31072.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080870 restraints weight = 21949.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081560 restraints weight = 16790.038| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27514 Z= 0.164 Angle : 0.715 12.997 37329 Z= 0.361 Chirality : 0.047 0.260 4425 Planarity : 0.005 0.065 4851 Dihedral : 7.058 123.740 3878 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.54 % 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: -1.73 (0.14), residues: 3544 helix: 0.15 (0.13), residues: 1498 sheet: -3.00 (0.21), residues: 491 loop : -1.74 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 22 TYR 0.023 0.002 TYR C 196 PHE 0.028 0.002 PHE A 292 TRP 0.007 0.002 TRP e 15 HIS 0.007 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27513) covalent geometry : angle 0.71474 / 0.36 (37327) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 1.41485 / 0.83 ( 2) hydrogen bonds : bond 0.04106 / 2.78 ( 1280) hydrogen bonds : angle 5.38831 / 3.69 ( 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 680 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 679 time to evaluate : 1.051 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: A 61 ILE cc_start: 0.8768 (pt) cc_final: 0.8156 (mt) REVERT: A 157 MET cc_start: 0.7789 (ttm) cc_final: 0.7537 (ttm) REVERT: A 296 SER cc_start: 0.8590 (t) cc_final: 0.7297 (t) REVERT: A 300 GLU cc_start: 0.8689 (tt0) cc_final: 0.7646 (tt0) REVERT: A 337 SER cc_start: 0.9082 (p) cc_final: 0.8725 (p) REVERT: A 348 ASP cc_start: 0.8738 (p0) cc_final: 0.8375 (p0) REVERT: A 436 MET cc_start: 0.8711 (ppp) cc_final: 0.8329 (ppp) REVERT: A 484 GLU cc_start: 0.8481 (mp0) cc_final: 0.7868 (tm-30) REVERT: A 498 MET cc_start: 0.8403 (tpt) cc_final: 0.7619 (tpt) REVERT: B 26 VAL cc_start: 0.7368 (t) cc_final: 0.7125 (t) REVERT: B 157 MET cc_start: 0.7488 (ttp) cc_final: 0.7246 (ttp) REVERT: B 194 CYS cc_start: 0.8157 (m) cc_final: 0.7693 (m) REVERT: B 274 MET cc_start: 0.8975 (ptm) cc_final: 0.8059 (tmm) REVERT: B 293 TYR cc_start: 0.7483 (t80) cc_final: 0.6453 (t80) REVERT: B 482 PHE cc_start: 0.7614 (p90) cc_final: 0.7328 (p90) REVERT: C 15 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7281 (mm-30) REVERT: C 49 MET cc_start: 0.7925 (tpt) cc_final: 0.7558 (tpt) REVERT: C 105 LEU cc_start: 0.9329 (mp) cc_final: 0.9098 (mp) REVERT: C 165 ARG cc_start: 0.5902 (ptp-170) cc_final: 0.5543 (ptp-170) REVERT: C 251 MET cc_start: 0.7480 (ttp) cc_final: 0.7142 (ttp) REVERT: C 274 MET cc_start: 0.7964 (mmm) cc_final: 0.7416 (mmm) REVERT: C 293 TYR cc_start: 0.8891 (t80) cc_final: 0.8608 (t80) REVERT: C 314 MET cc_start: 0.8570 (tpt) cc_final: 0.7923 (tpp) REVERT: C 385 LEU cc_start: 0.8607 (mt) cc_final: 0.8328 (mt) REVERT: C 484 GLU cc_start: 0.8351 (tp30) cc_final: 0.8068 (tp30) REVERT: D 63 CYS cc_start: 0.8249 (m) cc_final: 0.7957 (m) REVERT: D 182 ILE cc_start: 0.9177 (mm) cc_final: 0.8863 (mm) REVERT: D 236 TYR cc_start: 0.4767 (t80) cc_final: 0.4268 (t80) REVERT: D 239 MET cc_start: 0.8351 (mmm) cc_final: 0.7948 (mmt) REVERT: D 292 MET cc_start: 0.8017 (ttm) cc_final: 0.7513 (ttm) REVERT: D 335 THR cc_start: 0.8805 (t) cc_final: 0.8599 (m) REVERT: D 453 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 22 ARG cc_start: 0.7433 (mmp80) cc_final: 0.7088 (mmp80) REVERT: E 79 MET cc_start: 0.7857 (mpp) cc_final: 0.7643 (mpp) REVERT: E 89 MET cc_start: 0.7545 (mtt) cc_final: 0.7322 (mtt) REVERT: E 183 MET cc_start: 0.9085 (mtt) cc_final: 0.8879 (mtp) REVERT: E 212 LEU cc_start: 0.8494 (tp) cc_final: 0.8267 (tp) REVERT: E 248 ARG cc_start: 0.6875 (mmt180) cc_final: 0.6621 (mmt180) REVERT: E 299 GLN cc_start: 0.8359 (pm20) cc_final: 0.7713 (pm20) REVERT: E 343 PHE cc_start: 0.5976 (t80) cc_final: 0.5567 (t80) REVERT: E 393 GLU cc_start: 0.7999 (tt0) cc_final: 0.7617 (tp30) REVERT: F 79 MET cc_start: 0.8833 (mmt) cc_final: 0.8351 (mmm) REVERT: F 213 TYR cc_start: 0.8330 (t80) cc_final: 0.8065 (t80) REVERT: F 256 MET cc_start: 0.8318 (mmm) cc_final: 0.8001 (mmt) REVERT: F 328 TYR cc_start: 0.8116 (t80) cc_final: 0.7561 (t80) REVERT: F 486 LYS cc_start: 0.8993 (tttp) cc_final: 0.8527 (tppp) REVERT: d 77 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7969 (mtp180) REVERT: d 112 TYR cc_start: 0.7858 (t80) cc_final: 0.7657 (t80) REVERT: d 125 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8135 (mttp) REVERT: d 151 ASP cc_start: 0.7703 (m-30) cc_final: 0.7494 (m-30) REVERT: d 164 GLU cc_start: 0.7916 (mm-30) cc_final: 0.6688 (tp30) REVERT: d 193 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8471 (tt0) REVERT: g 302 SER cc_start: 0.9209 (t) cc_final: 0.9003 (t) REVERT: g 303 GLN cc_start: 0.8571 (tp40) cc_final: 0.8204 (tp40) REVERT: g 310 GLU cc_start: 0.8767 (tp30) cc_final: 0.8312 (tp30) REVERT: g 320 MET cc_start: 0.7988 (mmm) cc_final: 0.7723 (tpp) REVERT: g 354 LEU cc_start: 0.8422 (tt) cc_final: 0.8132 (pp) REVERT: e 19 VAL cc_start: 0.8084 (t) cc_final: 0.7761 (t) outliers start: 1 outliers final: 0 residues processed: 680 average time/residue: 0.1751 time to fit residues: 194.3213 Evaluate side-chains 501 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN B 186 ASN B 342 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 238 GLN ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 472 GLN d 141 HIS g 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076244 restraints weight = 85409.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078498 restraints weight = 48126.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079985 restraints weight = 30744.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081049 restraints weight = 21718.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081709 restraints weight = 16536.029| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27514 Z= 0.164 Angle : 0.727 13.676 37329 Z= 0.366 Chirality : 0.047 0.274 4425 Planarity : 0.005 0.064 4851 Dihedral : 7.065 126.447 3878 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % 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: -1.63 (0.14), residues: 3544 helix: 0.18 (0.13), residues: 1499 sheet: -2.86 (0.22), residues: 485 loop : -1.67 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 277 TYR 0.039 0.002 TYR A 287 PHE 0.032 0.002 PHE A 292 TRP 0.006 0.001 TRP e 15 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (27513) covalent geometry : angle 0.72675 / 0.37 (37327) SS BOND : bond 0.00169 / 0.09 ( 1) SS BOND : angle 1.06527 / 0.62 ( 2) hydrogen bonds : bond 0.04092 / 2.76 ( 1280) hydrogen bonds : angle 5.38145 / 3.67 ( 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 652 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 651 time to evaluate : 1.198 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 157 MET cc_start: 0.7710 (ttm) cc_final: 0.7472 (ttm) REVERT: A 292 PHE cc_start: 0.7797 (t80) cc_final: 0.7105 (t80) REVERT: A 296 SER cc_start: 0.8638 (t) cc_final: 0.7903 (t) REVERT: A 314 MET cc_start: 0.7428 (mmm) cc_final: 0.7167 (tpp) REVERT: A 337 SER cc_start: 0.8918 (p) cc_final: 0.8701 (p) REVERT: A 348 ASP cc_start: 0.8784 (p0) cc_final: 0.8451 (p0) REVERT: A 362 ILE cc_start: 0.8057 (tp) cc_final: 0.7844 (pt) REVERT: A 436 MET cc_start: 0.8734 (ppp) cc_final: 0.8508 (ppp) REVERT: A 484 GLU cc_start: 0.8503 (mp0) cc_final: 0.7777 (tm-30) REVERT: B 157 MET cc_start: 0.7506 (ttp) cc_final: 0.7277 (ttp) REVERT: B 194 CYS cc_start: 0.7965 (m) cc_final: 0.7543 (m) REVERT: B 274 MET cc_start: 0.8988 (ptm) cc_final: 0.7953 (tmm) REVERT: B 293 TYR cc_start: 0.7439 (t80) cc_final: 0.6396 (t80) REVERT: B 482 PHE cc_start: 0.7608 (p90) cc_final: 0.7365 (p90) REVERT: B 498 MET cc_start: 0.7717 (mtt) cc_final: 0.7145 (tpp) REVERT: C 15 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7221 (mm-30) REVERT: C 49 MET cc_start: 0.7937 (tpt) cc_final: 0.7627 (tpt) REVERT: C 105 LEU cc_start: 0.9331 (mp) cc_final: 0.9121 (mp) REVERT: C 251 MET cc_start: 0.7454 (ttp) cc_final: 0.7201 (ttp) REVERT: C 273 GLN cc_start: 0.8610 (tt0) cc_final: 0.7837 (tt0) REVERT: C 274 MET cc_start: 0.7970 (mmm) cc_final: 0.7487 (mmm) REVERT: C 314 MET cc_start: 0.8528 (tpt) cc_final: 0.8178 (tpp) REVERT: C 484 GLU cc_start: 0.8230 (tp30) cc_final: 0.7982 (tp30) REVERT: D 63 CYS cc_start: 0.8142 (m) cc_final: 0.7775 (m) REVERT: D 64 GLU cc_start: 0.6912 (mp0) cc_final: 0.6423 (mp0) REVERT: D 236 TYR cc_start: 0.4687 (t80) cc_final: 0.4227 (t80) REVERT: D 239 MET cc_start: 0.8326 (mmm) cc_final: 0.7921 (mmt) REVERT: D 292 MET cc_start: 0.7902 (ttm) cc_final: 0.7356 (ttm) REVERT: D 335 THR cc_start: 0.8883 (t) cc_final: 0.8610 (m) REVERT: D 366 ASP cc_start: 0.8098 (t0) cc_final: 0.6713 (t0) REVERT: D 426 LYS cc_start: 0.8407 (mttm) cc_final: 0.7598 (mttm) REVERT: D 453 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7749 (mm-30) REVERT: D 469 LEU cc_start: 0.8569 (mt) cc_final: 0.8291 (mt) REVERT: E 22 ARG cc_start: 0.7413 (mmp80) cc_final: 0.7053 (mmp80) REVERT: E 64 GLU cc_start: 0.6912 (pm20) cc_final: 0.6550 (pm20) REVERT: E 183 MET cc_start: 0.9069 (mtt) cc_final: 0.8865 (mtp) REVERT: E 251 LEU cc_start: 0.8253 (tp) cc_final: 0.8012 (tp) REVERT: E 283 SER cc_start: 0.8809 (t) cc_final: 0.8570 (t) REVERT: E 299 GLN cc_start: 0.8239 (pm20) cc_final: 0.7659 (pm20) REVERT: E 393 GLU cc_start: 0.8041 (tt0) cc_final: 0.7659 (tp30) REVERT: E 471 GLU cc_start: 0.8782 (pt0) cc_final: 0.8545 (pt0) REVERT: F 79 MET cc_start: 0.8778 (mmt) cc_final: 0.8320 (mmm) REVERT: F 213 TYR cc_start: 0.8319 (t80) cc_final: 0.8059 (t80) REVERT: F 254 LEU cc_start: 0.8719 (tp) cc_final: 0.8409 (tp) REVERT: F 277 ARG cc_start: 0.8463 (mmp80) cc_final: 0.7901 (mmp80) REVERT: F 374 MET cc_start: 0.8636 (mmt) cc_final: 0.8412 (mpp) REVERT: F 486 LYS cc_start: 0.9014 (tttp) cc_final: 0.8544 (tppp) REVERT: d 125 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8109 (mttp) REVERT: d 151 ASP cc_start: 0.7720 (m-30) cc_final: 0.7511 (m-30) REVERT: d 164 GLU cc_start: 0.7915 (mm-30) cc_final: 0.6628 (tp30) REVERT: d 193 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8519 (tt0) REVERT: d 210 LYS cc_start: 0.8625 (tptt) cc_final: 0.7966 (mmtm) REVERT: g 46 GLU cc_start: 0.7751 (mp0) cc_final: 0.6663 (pp20) REVERT: g 283 GLU cc_start: 0.7436 (pm20) cc_final: 0.7120 (mm-30) REVERT: g 310 GLU cc_start: 0.8810 (tp30) cc_final: 0.8283 (tp30) REVERT: g 320 MET cc_start: 0.8028 (mmm) cc_final: 0.7802 (tpp) REVERT: g 354 LEU cc_start: 0.8416 (tt) cc_final: 0.8089 (pp) REVERT: e 11 ASN cc_start: 0.8656 (p0) cc_final: 0.8318 (p0) REVERT: e 19 VAL cc_start: 0.8124 (t) cc_final: 0.7861 (t) outliers start: 1 outliers final: 0 residues processed: 651 average time/residue: 0.1760 time to fit residues: 187.1096 Evaluate side-chains 486 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 10.0000 chunk 289 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 216 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN g 301 ASN g 309 GLN e 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077677 restraints weight = 85237.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079922 restraints weight = 48015.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081456 restraints weight = 30600.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082462 restraints weight = 21558.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083087 restraints weight = 16508.218| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4946 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= 0.146 Angle : 0.736 14.144 37329 Z= 0.367 Chirality : 0.047 0.300 4425 Planarity : 0.005 0.070 4851 Dihedral : 6.947 126.024 3878 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -1.52 (0.14), residues: 3544 helix: 0.26 (0.13), residues: 1496 sheet: -2.73 (0.22), residues: 474 loop : -1.64 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 165 TYR 0.028 0.002 TYR A 287 PHE 0.033 0.002 PHE B 390 TRP 0.006 0.001 TRP e 15 HIS 0.006 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (27513) covalent geometry : angle 0.73594 / 0.37 (37327) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 1.04776 / 0.62 ( 2) hydrogen bonds : bond 0.03994 / 2.68 ( 1280) hydrogen bonds : angle 5.32206 / 3.63 ( 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 670 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 1.108 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 157 MET cc_start: 0.7676 (ttm) cc_final: 0.7381 (ttm) REVERT: A 292 PHE cc_start: 0.7497 (t80) cc_final: 0.6979 (t80) REVERT: A 296 SER cc_start: 0.8931 (t) cc_final: 0.7897 (t) REVERT: A 300 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 348 ASP cc_start: 0.8748 (p0) cc_final: 0.8238 (p0) REVERT: A 436 MET cc_start: 0.8711 (ppp) cc_final: 0.8466 (ppp) REVERT: A 484 GLU cc_start: 0.8513 (mp0) cc_final: 0.7751 (tm-30) REVERT: A 498 MET cc_start: 0.8012 (tpt) cc_final: 0.6896 (tpt) REVERT: B 34 GLN cc_start: 0.7652 (tp-100) cc_final: 0.6761 (tt0) REVERT: B 37 ASP cc_start: 0.7770 (m-30) cc_final: 0.7248 (m-30) REVERT: B 157 MET cc_start: 0.7449 (ttp) cc_final: 0.7199 (ttt) REVERT: B 194 CYS cc_start: 0.7870 (m) cc_final: 0.7407 (m) REVERT: B 274 MET cc_start: 0.8955 (ptm) cc_final: 0.7863 (tmm) REVERT: B 293 TYR cc_start: 0.7362 (t80) cc_final: 0.6285 (t80) REVERT: B 498 MET cc_start: 0.7716 (mtt) cc_final: 0.7108 (tpp) REVERT: C 15 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7132 (mm-30) REVERT: C 49 MET cc_start: 0.7927 (tpt) cc_final: 0.7656 (tpt) REVERT: C 251 MET cc_start: 0.7303 (ttp) cc_final: 0.7074 (ttp) REVERT: C 258 LEU cc_start: 0.9348 (tt) cc_final: 0.9133 (tt) REVERT: C 273 GLN cc_start: 0.8542 (tt0) cc_final: 0.7809 (tt0) REVERT: C 274 MET cc_start: 0.7925 (mmm) cc_final: 0.7310 (mmm) REVERT: C 314 MET cc_start: 0.8490 (tpt) cc_final: 0.7619 (tpp) REVERT: C 385 LEU cc_start: 0.8633 (mt) cc_final: 0.8325 (mt) REVERT: C 484 GLU cc_start: 0.8292 (tp30) cc_final: 0.7990 (tp30) REVERT: D 63 CYS cc_start: 0.8133 (m) cc_final: 0.7801 (m) REVERT: D 64 GLU cc_start: 0.7067 (mp0) cc_final: 0.6639 (mp0) REVERT: D 182 ILE cc_start: 0.9082 (mm) cc_final: 0.8813 (mm) REVERT: D 236 TYR cc_start: 0.4676 (t80) cc_final: 0.4379 (t80) REVERT: D 239 MET cc_start: 0.8278 (mmm) cc_final: 0.7931 (mmt) REVERT: D 247 MET cc_start: 0.8266 (ttt) cc_final: 0.7796 (ttm) REVERT: D 292 MET cc_start: 0.7797 (ttm) cc_final: 0.7375 (ttm) REVERT: D 335 THR cc_start: 0.8730 (t) cc_final: 0.8491 (m) REVERT: D 366 ASP cc_start: 0.8060 (t0) cc_final: 0.6785 (t0) REVERT: D 426 LYS cc_start: 0.8436 (mttm) cc_final: 0.7611 (mttm) REVERT: D 453 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 469 LEU cc_start: 0.8585 (mt) cc_final: 0.8303 (mt) REVERT: D 477 VAL cc_start: 0.9059 (p) cc_final: 0.8850 (t) REVERT: E 22 ARG cc_start: 0.7432 (mmp80) cc_final: 0.7063 (mmp80) REVERT: E 64 GLU cc_start: 0.6847 (pm20) cc_final: 0.6471 (pm20) REVERT: E 79 MET cc_start: 0.7638 (mpp) cc_final: 0.7233 (mpp) REVERT: E 80 SER cc_start: 0.9163 (m) cc_final: 0.8643 (t) REVERT: E 182 ILE cc_start: 0.9229 (mm) cc_final: 0.8998 (mt) REVERT: E 183 MET cc_start: 0.9083 (mtt) cc_final: 0.8795 (mtp) REVERT: E 299 GLN cc_start: 0.8191 (pm20) cc_final: 0.7591 (pm20) REVERT: E 393 GLU cc_start: 0.8045 (tt0) cc_final: 0.7628 (tp30) REVERT: F 59 MET cc_start: 0.7122 (tpp) cc_final: 0.6501 (tmm) REVERT: F 79 MET cc_start: 0.8847 (mmt) cc_final: 0.8301 (mmm) REVERT: F 154 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7269 (pttt) REVERT: F 213 TYR cc_start: 0.8313 (t80) cc_final: 0.8050 (t80) REVERT: F 254 LEU cc_start: 0.8667 (tp) cc_final: 0.8442 (tp) REVERT: F 486 LYS cc_start: 0.8981 (tttp) cc_final: 0.8559 (tppp) REVERT: d 104 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8262 (mtm180) REVERT: d 125 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8105 (mttp) REVERT: d 164 GLU cc_start: 0.7883 (mm-30) cc_final: 0.6306 (tp30) REVERT: d 193 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8510 (tt0) REVERT: d 210 LYS cc_start: 0.8377 (tptt) cc_final: 0.8003 (mmtm) REVERT: g 302 SER cc_start: 0.9216 (t) cc_final: 0.9012 (t) REVERT: g 303 GLN cc_start: 0.8475 (tp40) cc_final: 0.8118 (tp40) REVERT: g 320 MET cc_start: 0.7971 (mmm) cc_final: 0.7674 (tpp) REVERT: g 354 LEU cc_start: 0.8382 (tt) cc_final: 0.8071 (pp) REVERT: e 19 VAL cc_start: 0.8104 (t) cc_final: 0.7823 (t) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.1748 time to fit residues: 190.1779 Evaluate side-chains 494 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS B 186 ASN B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN D 187 ASN ** D 274 ASN ** 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 240 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS g 301 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076619 restraints weight = 86048.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.078863 restraints weight = 48662.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080385 restraints weight = 31248.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081395 restraints weight = 22068.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082077 restraints weight = 16930.790| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27514 Z= 0.166 Angle : 0.756 14.256 37329 Z= 0.376 Chirality : 0.048 0.311 4425 Planarity : 0.005 0.077 4851 Dihedral : 6.935 126.514 3878 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.07 % Allowed : 0.87 % Favored : 99.06 % 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: -1.54 (0.14), residues: 3544 helix: 0.21 (0.13), residues: 1505 sheet: -2.76 (0.22), residues: 480 loop : -1.60 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 172 TYR 0.026 0.002 TYR A 287 PHE 0.031 0.002 PHE B 390 TRP 0.005 0.001 TRP e 15 HIS 0.006 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (27513) covalent geometry : angle 0.75624 / 0.38 (37327) SS BOND : bond 0.00207 / 0.11 ( 1) SS BOND : angle 1.01405 / 0.60 ( 2) hydrogen bonds : bond 0.04054 / 2.73 ( 1280) hydrogen bonds : angle 5.28979 / 3.61 ( 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 636 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 634 time to evaluate : 1.127 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 157 MET cc_start: 0.7646 (ttm) cc_final: 0.7317 (ttm) REVERT: A 158 ILE cc_start: 0.9364 (mp) cc_final: 0.8972 (tt) REVERT: A 292 PHE cc_start: 0.7386 (t80) cc_final: 0.6750 (t80) REVERT: A 296 SER cc_start: 0.8899 (t) cc_final: 0.7604 (t) REVERT: A 314 MET cc_start: 0.7230 (tpt) cc_final: 0.7027 (tpt) REVERT: A 348 ASP cc_start: 0.8752 (p0) cc_final: 0.8246 (p0) REVERT: A 349 LEU cc_start: 0.9183 (mt) cc_final: 0.8969 (mt) REVERT: A 360 VAL cc_start: 0.8001 (m) cc_final: 0.7580 (m) REVERT: A 436 MET cc_start: 0.8797 (ppp) cc_final: 0.8520 (ppp) REVERT: A 484 GLU cc_start: 0.8510 (mp0) cc_final: 0.7738 (tm-30) REVERT: A 498 MET cc_start: 0.8028 (tpt) cc_final: 0.6972 (tpt) REVERT: B 34 GLN cc_start: 0.7725 (tp-100) cc_final: 0.6861 (tt0) REVERT: B 194 CYS cc_start: 0.7794 (m) cc_final: 0.7346 (m) REVERT: B 238 LEU cc_start: 0.8841 (pp) cc_final: 0.8602 (mm) REVERT: B 293 TYR cc_start: 0.7417 (t80) cc_final: 0.6385 (t80) REVERT: B 392 GLU cc_start: 0.7322 (pp20) cc_final: 0.6824 (pp20) REVERT: C 15 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7145 (mm-30) REVERT: C 49 MET cc_start: 0.7994 (tpt) cc_final: 0.7692 (tpt) REVERT: C 105 LEU cc_start: 0.9282 (mp) cc_final: 0.9000 (mp) REVERT: C 251 MET cc_start: 0.7335 (ttp) cc_final: 0.7116 (ttp) REVERT: C 266 LYS cc_start: 0.8359 (mmpt) cc_final: 0.7988 (mmtt) REVERT: C 274 MET cc_start: 0.8002 (mmm) cc_final: 0.7478 (mmm) REVERT: C 314 MET cc_start: 0.8689 (tpt) cc_final: 0.7799 (tpp) REVERT: C 385 LEU cc_start: 0.8639 (mt) cc_final: 0.8321 (mt) REVERT: C 433 GLU cc_start: 0.6754 (tp30) cc_final: 0.6114 (tp30) REVERT: C 484 GLU cc_start: 0.8278 (tp30) cc_final: 0.7968 (tp30) REVERT: D 63 CYS cc_start: 0.8197 (m) cc_final: 0.7719 (m) REVERT: D 64 GLU cc_start: 0.7103 (mp0) cc_final: 0.6824 (mp0) REVERT: D 182 ILE cc_start: 0.9072 (mm) cc_final: 0.8827 (mm) REVERT: D 236 TYR cc_start: 0.4747 (t80) cc_final: 0.4429 (t80) REVERT: D 239 MET cc_start: 0.8325 (mmm) cc_final: 0.7947 (mmt) REVERT: D 285 VAL cc_start: 0.9482 (t) cc_final: 0.9177 (t) REVERT: D 292 MET cc_start: 0.7967 (ttm) cc_final: 0.7542 (ttm) REVERT: D 335 THR cc_start: 0.8835 (t) cc_final: 0.8607 (m) REVERT: D 366 ASP cc_start: 0.8163 (t0) cc_final: 0.6917 (t0) REVERT: D 426 LYS cc_start: 0.8417 (mttm) cc_final: 0.7602 (mttm) REVERT: D 453 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7803 (mm-30) REVERT: D 469 LEU cc_start: 0.8593 (mt) cc_final: 0.8231 (mt) REVERT: E 22 ARG cc_start: 0.7416 (mmp80) cc_final: 0.7061 (mmp80) REVERT: E 64 GLU cc_start: 0.6888 (pm20) cc_final: 0.6471 (pm20) REVERT: E 79 MET cc_start: 0.7644 (mpp) cc_final: 0.7233 (mpp) REVERT: E 80 SER cc_start: 0.9142 (m) cc_final: 0.8659 (t) REVERT: E 182 ILE cc_start: 0.9190 (mm) cc_final: 0.8920 (mt) REVERT: E 251 LEU cc_start: 0.8173 (tp) cc_final: 0.7943 (tp) REVERT: E 283 SER cc_start: 0.8950 (t) cc_final: 0.8657 (t) REVERT: E 299 GLN cc_start: 0.8282 (pm20) cc_final: 0.7643 (pm20) REVERT: F 79 MET cc_start: 0.8892 (mmt) cc_final: 0.8334 (mmm) REVERT: F 213 TYR cc_start: 0.8379 (t80) cc_final: 0.8065 (t80) REVERT: F 254 LEU cc_start: 0.8750 (tp) cc_final: 0.8528 (tp) REVERT: F 486 LYS cc_start: 0.9030 (tttp) cc_final: 0.8571 (tppp) REVERT: d 77 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7854 (mtp180) REVERT: d 104 ARG cc_start: 0.8607 (tpt170) cc_final: 0.8261 (mtm180) REVERT: d 113 TYR cc_start: 0.8731 (t80) cc_final: 0.8528 (t80) REVERT: d 125 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8100 (mttp) REVERT: d 164 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6463 (tp30) REVERT: d 193 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8532 (tt0) REVERT: d 210 LYS cc_start: 0.8409 (tptt) cc_final: 0.8039 (mmtm) REVERT: g 283 GLU cc_start: 0.7396 (pm20) cc_final: 0.6977 (mm-30) REVERT: g 303 GLN cc_start: 0.8549 (tp40) cc_final: 0.8194 (tp40) REVERT: g 320 MET cc_start: 0.8105 (mmm) cc_final: 0.7805 (tpp) REVERT: g 354 LEU cc_start: 0.8396 (tt) cc_final: 0.8118 (pp) REVERT: e 19 VAL cc_start: 0.8137 (t) cc_final: 0.7889 (t) REVERT: e 130 ASN cc_start: 0.4785 (m-40) cc_final: 0.4513 (m-40) outliers start: 2 outliers final: 1 residues processed: 635 average time/residue: 0.1745 time to fit residues: 180.9212 Evaluate side-chains 489 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 4.9990 chunk 126 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 497 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** 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** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN g 301 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076599 restraints weight = 85925.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078868 restraints weight = 48745.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080367 restraints weight = 31271.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081309 restraints weight = 22183.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082076 restraints weight = 17246.071| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27514 Z= 0.161 Angle : 0.772 14.502 37329 Z= 0.381 Chirality : 0.048 0.331 4425 Planarity : 0.005 0.114 4851 Dihedral : 6.935 130.760 3878 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -1.53 (0.14), residues: 3544 helix: 0.21 (0.13), residues: 1516 sheet: -2.71 (0.22), residues: 474 loop : -1.63 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 280 TYR 0.039 0.002 TYR A 287 PHE 0.031 0.002 PHE E 343 TRP 0.006 0.001 TRP e 15 HIS 0.005 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (27513) covalent geometry : angle 0.77164 / 0.38 (37327) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 1.11274 / 0.65 ( 2) hydrogen bonds : bond 0.04026 / 2.71 ( 1280) hydrogen bonds : angle 5.30557 / 3.62 ( 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 638 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 1.109 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: A 157 MET cc_start: 0.7595 (ttm) cc_final: 0.7342 (ttm) REVERT: A 158 ILE cc_start: 0.9344 (mp) cc_final: 0.8989 (tt) REVERT: A 292 PHE cc_start: 0.7348 (t80) cc_final: 0.6641 (t80) REVERT: A 348 ASP cc_start: 0.8735 (p0) cc_final: 0.8249 (p0) REVERT: A 349 LEU cc_start: 0.9173 (mt) cc_final: 0.8973 (mt) REVERT: A 360 VAL cc_start: 0.7952 (m) cc_final: 0.7508 (m) REVERT: A 436 MET cc_start: 0.8805 (ppp) cc_final: 0.8467 (ppp) REVERT: A 457 TYR cc_start: 0.5822 (t80) cc_final: 0.3828 (t80) REVERT: A 484 GLU cc_start: 0.8465 (mp0) cc_final: 0.7746 (tm-30) REVERT: A 498 MET cc_start: 0.8002 (tpt) cc_final: 0.6929 (tpt) REVERT: B 34 GLN cc_start: 0.7704 (tp-100) cc_final: 0.6817 (tt0) REVERT: B 293 TYR cc_start: 0.7480 (t80) cc_final: 0.6386 (t80) REVERT: B 392 GLU cc_start: 0.7228 (pp20) cc_final: 0.6839 (pp20) REVERT: B 498 MET cc_start: 0.7667 (mtt) cc_final: 0.7406 (mmt) REVERT: C 15 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7165 (mm-30) REVERT: C 49 MET cc_start: 0.8007 (tpt) cc_final: 0.7671 (tpt) REVERT: C 105 LEU cc_start: 0.9270 (mp) cc_final: 0.9018 (mp) REVERT: C 274 MET cc_start: 0.7965 (mmm) cc_final: 0.7315 (mmm) REVERT: C 314 MET cc_start: 0.8652 (tpt) cc_final: 0.7773 (tpp) REVERT: C 484 GLU cc_start: 0.8194 (tp30) cc_final: 0.7878 (tp30) REVERT: D 63 CYS cc_start: 0.8211 (m) cc_final: 0.7756 (m) REVERT: D 64 GLU cc_start: 0.7057 (mp0) cc_final: 0.6739 (mp0) REVERT: D 182 ILE cc_start: 0.9060 (mm) cc_final: 0.8853 (mm) REVERT: D 236 TYR cc_start: 0.4672 (t80) cc_final: 0.4391 (t80) REVERT: D 239 MET cc_start: 0.8252 (mmm) cc_final: 0.7844 (mmt) REVERT: D 285 VAL cc_start: 0.9500 (t) cc_final: 0.9158 (t) REVERT: D 292 MET cc_start: 0.7935 (ttm) cc_final: 0.7530 (ttm) REVERT: D 335 THR cc_start: 0.8828 (t) cc_final: 0.8607 (m) REVERT: D 366 ASP cc_start: 0.8172 (t0) cc_final: 0.6962 (t0) REVERT: D 426 LYS cc_start: 0.8391 (mttm) cc_final: 0.7601 (mttm) REVERT: D 453 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 469 LEU cc_start: 0.8592 (mt) cc_final: 0.8218 (mt) REVERT: E 22 ARG cc_start: 0.7497 (mmp80) cc_final: 0.7118 (mmp80) REVERT: E 64 GLU cc_start: 0.6878 (pm20) cc_final: 0.6432 (pm20) REVERT: E 79 MET cc_start: 0.7654 (mpp) cc_final: 0.7243 (mpp) REVERT: E 80 SER cc_start: 0.9085 (m) cc_final: 0.8649 (t) REVERT: E 182 ILE cc_start: 0.9141 (mm) cc_final: 0.8901 (mt) REVERT: E 283 SER cc_start: 0.8891 (t) cc_final: 0.8585 (t) REVERT: E 299 GLN cc_start: 0.8252 (pm20) cc_final: 0.7664 (pm20) REVERT: F 79 MET cc_start: 0.8899 (mmt) cc_final: 0.8268 (mmm) REVERT: F 154 LYS cc_start: 0.7821 (ptpp) cc_final: 0.7348 (pttt) REVERT: F 184 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7697 (tt0) REVERT: F 213 TYR cc_start: 0.8447 (t80) cc_final: 0.8223 (t80) REVERT: F 247 MET cc_start: 0.8272 (tpp) cc_final: 0.7995 (tpp) REVERT: F 254 LEU cc_start: 0.8759 (tp) cc_final: 0.8546 (tp) REVERT: F 486 LYS cc_start: 0.9000 (tttp) cc_final: 0.8529 (tppp) REVERT: d 104 ARG cc_start: 0.8620 (tpt170) cc_final: 0.8276 (mtm180) REVERT: d 125 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8121 (mttp) REVERT: d 162 LEU cc_start: 0.8840 (mt) cc_final: 0.8303 (tt) REVERT: d 164 GLU cc_start: 0.7799 (mm-30) cc_final: 0.6265 (tp30) REVERT: d 193 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8529 (tt0) REVERT: d 210 LYS cc_start: 0.8476 (tptt) cc_final: 0.8107 (mmtm) REVERT: g 46 GLU cc_start: 0.8117 (mp0) cc_final: 0.6824 (pp20) REVERT: g 283 GLU cc_start: 0.7375 (pm20) cc_final: 0.6971 (mm-30) REVERT: g 303 GLN cc_start: 0.8529 (tp40) cc_final: 0.8192 (tp40) REVERT: g 320 MET cc_start: 0.8018 (mmm) cc_final: 0.7730 (tpp) REVERT: g 354 LEU cc_start: 0.8427 (tt) cc_final: 0.8148 (pp) REVERT: e 19 VAL cc_start: 0.8087 (t) cc_final: 0.7872 (t) REVERT: e 130 ASN cc_start: 0.4786 (m-40) cc_final: 0.4478 (m-40) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.1723 time to fit residues: 180.2619 Evaluate side-chains 486 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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: 0.0570 chunk 211 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 271 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 253 optimal weight: 0.0010 chunk 69 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 244 optimal weight: 0.0470 chunk 176 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 295 HIS B 342 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 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 479 ASN F 67 GLN F 240 ASN ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080054 restraints weight = 83790.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082322 restraints weight = 47830.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083813 restraints weight = 30795.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084880 restraints weight = 21898.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085561 restraints weight = 16765.088| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27514 Z= 0.138 Angle : 0.768 15.373 37329 Z= 0.378 Chirality : 0.048 0.320 4425 Planarity : 0.005 0.121 4851 Dihedral : 6.860 133.047 3878 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % 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: 0.29 (0.13), residues: 1502 sheet: -2.67 (0.23), residues: 451 loop : -1.56 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 207 TYR 0.024 0.002 TYR A 287 PHE 0.026 0.002 PHE B 390 TRP 0.009 0.002 TRP e 15 HIS 0.006 0.001 HIS g 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (27513) covalent geometry : angle 0.76751 / 0.38 (37327) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.84790 / 0.50 ( 2) hydrogen bonds : bond 0.03915 / 2.61 ( 1280) hydrogen bonds : angle 5.26559 / 3.60 ( 3714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.59 seconds wall clock time: 87 minutes 38.06 seconds (5258.06 seconds total)