Starting phenix.real_space_refine on Sat Jul 4 14:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010.map" model { file = "/net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubl_64010/07_2026/9ubl_64010_neut_trim.cif" } resolution = 2.77 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= 0.019 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 24 5.49 5 Mg 6 5.21 5 S 80 5.16 5 C 12987 2.51 5 N 3775 2.21 5 O 3775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20653 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4199 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 498} Chain breaks: 9 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4038 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480} Chain breaks: 9 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3027 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 361} Chain: "D" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3034 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 362} Chain: "E" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2995 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 357} Chain: "F" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3030 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 361} Chain: "J" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 3} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.35, per 1000 atoms: 0.21 Number of scatterers: 20653 At special positions: 0 Unit cell: (96.928, 126.752, 175.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 80 16.00 P 24 15.00 Mg 6 11.99 O 3775 8.00 N 3775 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 100 " 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: 1.36 Conformation dependent library (CDL) restraints added in 849.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 260 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 262 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 461 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 262 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 461 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 260 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 260 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 461 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 262 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 260 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 262 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 461 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 461 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 260 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 461 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 260 " 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 9 sheets defined 58.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.931A pdb=" N GLN A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.729A pdb=" N GLU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 3.819A pdb=" N HIS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 81 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.785A pdb=" N GLN A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.741A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 217 removed outlier: 4.550A pdb=" N GLU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.914A pdb=" N LYS A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.654A pdb=" N ARG A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.117A pdb=" N ILE A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.955A pdb=" N ILE A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 540 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.859A pdb=" N ARG B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 Processing helix chain 'B' and resid 93 through 96 Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.730A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 215 Processing helix chain 'B' and resid 216 through 222 removed outlier: 4.954A pdb=" N SER B 220 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.574A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 305 through 313 removed outlier: 4.258A pdb=" N ARG B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 342 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 405 through 420 Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.958A pdb=" N ILE B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.612A pdb=" N THR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.671A pdb=" N ALA C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.509A pdb=" N GLU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 removed outlier: 4.141A pdb=" N GLY C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 343 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.676A pdb=" N GLU C 399 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.001A pdb=" N ARG C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 removed outlier: 3.860A pdb=" N GLU C 435 " --> pdb=" O ALA C 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 432 through 435' Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 467 through 478 Processing helix chain 'C' and resid 488 through 491 removed outlier: 3.626A pdb=" N ARG C 491 " --> pdb=" O HIS C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 509 through 517 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 306 through 314 removed outlier: 4.019A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 323 removed outlier: 3.837A pdb=" N LYS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 324 through 343 Processing helix chain 'D' and resid 352 through 357 removed outlier: 3.789A pdb=" N TYR D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 381 Processing helix chain 'D' and resid 403 through 420 Processing helix chain 'D' and resid 432 through 435 removed outlier: 3.649A pdb=" N GLU D 435 " --> pdb=" O ALA D 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.606A pdb=" N GLY D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 477 Processing helix chain 'D' and resid 488 through 491 removed outlier: 3.638A pdb=" N ARG D 491 " --> pdb=" O HIS D 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 556 through 568 removed outlier: 4.073A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 590 through 602 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.664A pdb=" N HIS E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 254 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 270 through 279 Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 305 through 314 removed outlier: 4.085A pdb=" N ARG E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY E 314 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 323 removed outlier: 3.735A pdb=" N LYS E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 320 through 323' Processing helix chain 'E' and resid 324 through 343 Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 362 through 381 Processing helix chain 'E' and resid 403 through 420 removed outlier: 3.769A pdb=" N ALA E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 removed outlier: 4.092A pdb=" N GLU E 435 " --> pdb=" O ALA E 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'E' and resid 436 through 446 Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 540 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.084A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 Processing helix chain 'E' and resid 590 through 602 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.223A pdb=" N TRP F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.909A pdb=" N LEU F 273 " --> pdb=" O HIS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.905A pdb=" N LYS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 362 through 381 Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.752A pdb=" N GLU F 399 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 420 removed outlier: 3.647A pdb=" N ARG F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 436 Processing helix chain 'F' and resid 437 through 445 removed outlier: 3.790A pdb=" N ALA F 441 " --> pdb=" O ARG F 437 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA F 442 " --> pdb=" O THR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 455 Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 532 through 540 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.583A pdb=" N THR F 564 " --> pdb=" O ASN F 560 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 590 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.665A pdb=" N GLU A 123 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.258A pdb=" N VAL A 32 " --> pdb=" O SER A 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 256 through 262 removed outlier: 7.507A pdb=" N LYS A 256 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 347 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A 258 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 349 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N HIS A 260 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N CYS A 351 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N HIS A 262 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N VAL A 389 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N GLY A 428 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 391 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 430 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 393 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 432 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 32 removed outlier: 5.713A pdb=" N LEU B 4 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 3 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N CYS B 100 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 5 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 262 removed outlier: 7.530A pdb=" N LYS B 256 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA B 347 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B 258 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE B 349 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N HIS B 260 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N CYS B 351 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N HIS B 262 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 345 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASN B 390 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA B 347 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 392 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 349 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR B 394 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 351 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR B 396 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 426 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B 391 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 428 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 427 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B 459 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 429 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N HIS B 461 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 431 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 483 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 256 through 262 removed outlier: 4.535A pdb=" N VAL C 257 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLU C 348 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 259 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG C 350 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS C 261 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N VAL C 389 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N GLY C 428 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 391 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASP C 430 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 393 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 483 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 262 removed outlier: 7.433A pdb=" N LYS D 256 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA D 347 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU D 258 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE D 349 " --> pdb=" O GLU D 258 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N HIS D 260 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N CYS D 351 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N HIS D 262 " --> pdb=" O CYS D 351 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N VAL D 389 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N GLY D 428 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU D 391 " --> pdb=" O GLY D 428 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP D 430 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 393 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 483 " --> pdb=" O GLU D 507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 256 through 262 removed outlier: 5.880A pdb=" N LYS E 256 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E 346 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS E 260 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ARG E 350 " --> pdb=" O HIS E 260 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS E 262 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA E 345 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASN E 390 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA E 347 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU E 392 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE E 349 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 394 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS E 351 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 256 through 262 removed outlier: 7.626A pdb=" N LYS F 256 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA F 347 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU F 258 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE F 349 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N HIS F 260 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N CYS F 351 " --> pdb=" O HIS F 260 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N HIS F 262 " --> pdb=" O CYS F 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA F 345 " --> pdb=" O HIS F 388 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN F 390 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA F 347 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU F 392 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE F 349 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 394 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS F 351 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 426 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 391 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY F 428 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2769 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: 3.48 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7038 1.34 - 1.46: 3931 1.46 - 1.58: 10035 1.58 - 1.69: 41 1.69 - 1.81: 106 Bond restraints: 21151 Sorted by residual: bond pdb=" C ARG A 199 " pdb=" N GLN A 200 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.27e-02 6.20e+03 2.11e+00 bond pdb=" C1' ATP F 701 " pdb=" O4' ATP F 701 " ideal model delta sigma weight residual 1.416 1.399 0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" N GLN A 200 " pdb=" CA GLN A 200 " ideal model delta sigma weight residual 1.459 1.475 -0.016 1.19e-02 7.06e+03 1.73e+00 bond pdb=" CA VAL A 606 " pdb=" CB VAL A 606 " ideal model delta sigma weight residual 1.537 1.522 0.015 1.29e-02 6.01e+03 1.31e+00 bond pdb=" C1' ATP D 701 " pdb=" O4' ATP D 701 " ideal model delta sigma weight residual 1.416 1.403 0.013 1.30e-02 5.92e+03 1.06e+00 ... (remaining 21146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 28306 1.53 - 3.06: 441 3.06 - 4.58: 114 4.58 - 6.11: 22 6.11 - 7.64: 7 Bond angle restraints: 28890 Sorted by residual: angle pdb=" CA MET A 19 " pdb=" CB MET A 19 " pdb=" CG MET A 19 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLU D 524 " pdb=" CA GLU D 524 " pdb=" C GLU D 524 " ideal model delta sigma weight residual 114.04 110.10 3.94 1.24e+00 6.50e-01 1.01e+01 angle pdb=" N GLU C 524 " pdb=" CA GLU C 524 " pdb=" C GLU C 524 " ideal model delta sigma weight residual 114.04 110.26 3.78 1.24e+00 6.50e-01 9.28e+00 angle pdb=" N MET A 19 " pdb=" CA MET A 19 " pdb=" CB MET A 19 " ideal model delta sigma weight residual 110.22 114.78 -4.56 1.54e+00 4.22e-01 8.75e+00 angle pdb=" N GLN A 200 " pdb=" CA GLN A 200 " pdb=" C GLN A 200 " ideal model delta sigma weight residual 111.07 108.22 2.85 1.07e+00 8.73e-01 7.10e+00 ... (remaining 28885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 11630 23.95 - 47.90: 968 47.90 - 71.85: 195 71.85 - 95.80: 29 95.80 - 119.75: 3 Dihedral angle restraints: 12825 sinusoidal: 5301 harmonic: 7524 Sorted by residual: dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 100 " pdb=" CB CYS A 100 " ideal model delta sinusoidal sigma weight residual -86.00 -28.58 -57.42 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CA ALA E 395 " pdb=" C ALA E 395 " pdb=" N THR E 396 " pdb=" CA THR E 396 " ideal model delta harmonic sigma weight residual -180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CG ARG C 497 " pdb=" CD ARG C 497 " pdb=" NE ARG C 497 " pdb=" CZ ARG C 497 " ideal model delta sinusoidal sigma weight residual 90.00 40.87 49.13 2 1.50e+01 4.44e-03 1.22e+01 ... (remaining 12822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2803 0.057 - 0.114: 389 0.114 - 0.171: 21 0.171 - 0.228: 0 0.228 - 0.286: 18 Chirality restraints: 3231 Sorted by residual: chirality pdb=" C3' ATP E 701 " pdb=" C2' ATP E 701 " pdb=" C4' ATP E 701 " pdb=" O3' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' ATP D 701 " pdb=" C2' ATP D 701 " pdb=" C4' ATP D 701 " pdb=" O3' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' ATP B 701 " pdb=" C2' ATP B 701 " pdb=" C4' ATP B 701 " pdb=" O3' ATP B 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 3228 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 231 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO E 232 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 232 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 232 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 243 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO D 244 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 244 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 244 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 41 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO B 42 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.018 5.00e-02 4.00e+02 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 118 2.41 - 3.03: 13297 3.03 - 3.65: 31374 3.65 - 4.28: 48843 4.28 - 4.90: 81680 Nonbonded interactions: 175312 Sorted by model distance: nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 1.782 2.170 nonbonded pdb=" OH TYR F 310 " pdb=" OG SER F 553 " model vdw 1.928 3.040 nonbonded pdb=" O3B ATP B 701 " pdb="MG MG B 702 " model vdw 1.960 2.170 nonbonded pdb=" OH TYR E 310 " pdb=" OG SER E 553 " model vdw 1.974 3.040 nonbonded pdb=" O3B ATP D 701 " pdb="MG MG D 702 " model vdw 2.001 2.170 ... (remaining 175307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 6 or (resid 12 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 34 or resid 38 through 60 \ or resid 73 through 125 or resid 145 through 397 or resid 404 through 433 or re \ sid 447 through 703)) selection = (chain 'B' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 100 or resid 106 through 125 or res \ id 145 through 153 or resid 159 through 173 or resid 198 through 703)) } ncs_group { reference = (chain 'C' and (resid 221 through 605 or resid 701 through 703)) selection = (chain 'D' and (resid 221 through 605 or resid 701 through 703)) selection = chain 'E' selection = (chain 'F' and (resid 221 through 605 or resid 701 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 0.004 0.028 21170 Z= 0.169 Angle : 0.519 7.639 28892 Z= 0.271 Chirality : 0.043 0.286 3231 Planarity : 0.003 0.042 3738 Dihedral : 17.686 119.748 7926 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.83 % Favored : 95.86 % Rotamer: Outliers : 2.37 % Allowed : 24.17 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2558 helix: 2.22 (0.15), residues: 1282 sheet: 0.12 (0.34), residues: 237 loop : 0.48 (0.21), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 385 TYR 0.011 0.001 TYR C 336 PHE 0.009 0.001 PHE D 476 TRP 0.012 0.001 TRP A 167 HIS 0.012 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (21151) covalent geometry : angle 0.51895 / 0.27 (28890) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.84154 / 0.49 ( 2) hydrogen bonds : bond 0.15393 / 9.79 ( 986) hydrogen bonds : angle 6.13328 / 4.44 ( 2769) metal coordination : bond 0.00434 / 0.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.5012 (mtm-85) cc_final: 0.3800 (pmt-80) REVERT: A 90 ARG cc_start: 0.7928 (mmm160) cc_final: 0.6891 (mmm160) REVERT: A 397 ARG cc_start: 0.7416 (tpp-160) cc_final: 0.6665 (ttp-170) REVERT: B 39 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7724 (pttt) REVERT: B 350 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8684 (mtt90) REVERT: B 467 ASP cc_start: 0.7929 (t0) cc_final: 0.7714 (p0) REVERT: B 472 TRP cc_start: 0.8705 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: B 477 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8679 (tttt) REVERT: D 403 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7977 (mtm110) REVERT: E 236 ARG cc_start: 0.6757 (ppt170) cc_final: 0.6332 (ppt170) REVERT: E 361 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7677 (mtm180) REVERT: F 443 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (mtt) outliers start: 50 outliers final: 21 residues processed: 269 average time/residue: 0.8129 time to fit residues: 241.6292 Evaluate side-chains 177 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 361 ARG Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 595 LYS Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 461 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN D 316 ASN E 234 HIS E 390 ASN F 390 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076899 restraints weight = 36332.833| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.76 r_work: 0.2794 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21170 Z= 0.175 Angle : 0.614 9.283 28892 Z= 0.312 Chirality : 0.042 0.222 3231 Planarity : 0.005 0.104 3738 Dihedral : 8.999 108.580 3155 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.32 % Favored : 96.29 % Rotamer: Outliers : 3.93 % Allowed : 21.33 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2558 helix: 1.98 (0.15), residues: 1297 sheet: 0.14 (0.35), residues: 227 loop : 0.42 (0.21), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 408 TYR 0.028 0.002 TYR B 50 PHE 0.013 0.001 PHE B 448 TRP 0.015 0.001 TRP A 364 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (21151) covalent geometry : angle 0.61362 / 0.31 (28890) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 0.62312 / 0.33 ( 2) hydrogen bonds : bond 0.04711 / 3.12 ( 986) hydrogen bonds : angle 5.12771 / 3.69 ( 2769) metal coordination : bond 0.00248 / 0.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 160 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7853 (mpt) cc_final: 0.7558 (mpp) REVERT: A 54 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.5969 (m90) REVERT: A 86 TRP cc_start: 0.9016 (t60) cc_final: 0.8399 (t60) REVERT: A 87 LEU cc_start: 0.9405 (mm) cc_final: 0.9201 (mm) REVERT: A 90 ARG cc_start: 0.8161 (mmm160) cc_final: 0.6918 (mmm160) REVERT: A 300 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9152 (mm) REVERT: A 303 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (pp20) REVERT: A 397 ARG cc_start: 0.6859 (tpp-160) cc_final: 0.5894 (ttp-170) REVERT: B 33 LEU cc_start: 0.6419 (mm) cc_final: 0.5980 (mm) REVERT: B 39 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7689 (pttt) REVERT: B 46 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (tp40) REVERT: B 53 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6522 (tmm) REVERT: B 350 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8465 (mtt90) REVERT: B 472 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: B 477 LYS cc_start: 0.9236 (mmpt) cc_final: 0.8389 (tttt) REVERT: B 491 ARG cc_start: 0.8762 (mtp-110) cc_final: 0.7758 (mtm180) REVERT: B 573 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7618 (mtt90) REVERT: C 290 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7878 (ttm170) REVERT: C 461 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7474 (m-70) REVERT: C 525 GLN cc_start: 0.8826 (tp40) cc_final: 0.8574 (pp30) REVERT: D 501 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8317 (mm-30) REVERT: E 236 ARG cc_start: 0.6941 (ppt170) cc_final: 0.6521 (ppt170) REVERT: E 246 GLN cc_start: 0.8288 (mp10) cc_final: 0.8049 (mp10) REVERT: E 603 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7069 (mp10) outliers start: 83 outliers final: 30 residues processed: 228 average time/residue: 0.7235 time to fit residues: 184.8830 Evaluate side-chains 184 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 461 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 164 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS F 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.077364 restraints weight = 36291.604| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.75 r_work: 0.2806 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21170 Z= 0.133 Angle : 0.544 9.364 28892 Z= 0.275 Chirality : 0.040 0.235 3231 Planarity : 0.005 0.097 3738 Dihedral : 8.564 107.844 3125 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.09 % Favored : 96.52 % Rotamer: Outliers : 3.03 % Allowed : 21.95 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.17), residues: 2558 helix: 2.04 (0.15), residues: 1306 sheet: 0.14 (0.34), residues: 242 loop : 0.46 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 403 TYR 0.012 0.001 TYR B 50 PHE 0.017 0.001 PHE A 79 TRP 0.013 0.001 TRP A 364 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21151) covalent geometry : angle 0.54358 / 0.27 (28890) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.36696 / 0.21 ( 2) hydrogen bonds : bond 0.04034 / 2.66 ( 986) hydrogen bonds : angle 4.79382 / 3.45 ( 2769) metal coordination : bond 0.00193 / 0.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6956 (tpp) cc_final: 0.6688 (tpp) REVERT: A 54 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6035 (m90) REVERT: A 86 TRP cc_start: 0.9014 (t60) cc_final: 0.8331 (t60) REVERT: A 90 ARG cc_start: 0.8116 (mmm160) cc_final: 0.6869 (mmm160) REVERT: A 300 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9154 (mm) REVERT: A 303 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8796 (pp20) REVERT: A 397 ARG cc_start: 0.6789 (tpp-160) cc_final: 0.5890 (ttp-170) REVERT: B 39 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7703 (pttt) REVERT: B 53 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6556 (tmm) REVERT: B 350 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8485 (mtt90) REVERT: B 477 LYS cc_start: 0.9243 (mmpt) cc_final: 0.8436 (tttt) REVERT: C 271 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 290 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7848 (ttm170) REVERT: C 418 GLU cc_start: 0.8579 (tt0) cc_final: 0.8336 (tt0) REVERT: C 461 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7436 (m-70) REVERT: C 525 GLN cc_start: 0.8841 (tp40) cc_final: 0.8584 (pp30) REVERT: D 350 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: D 397 ARG cc_start: 0.7420 (pmt-80) cc_final: 0.6639 (pmt-80) REVERT: D 418 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8085 (tp30) REVERT: D 501 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8343 (mm-30) REVERT: E 236 ARG cc_start: 0.6879 (ppt170) cc_final: 0.6506 (ppt170) REVERT: E 246 GLN cc_start: 0.8265 (mp10) cc_final: 0.8037 (mp10) REVERT: E 418 GLU cc_start: 0.8272 (tp30) cc_final: 0.8023 (tp30) REVERT: E 603 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: F 307 LEU cc_start: 0.8361 (tp) cc_final: 0.8115 (tp) REVERT: F 342 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8658 (t0) outliers start: 64 outliers final: 24 residues processed: 210 average time/residue: 0.7237 time to fit residues: 170.5043 Evaluate side-chains 181 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 31 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076306 restraints weight = 36639.461| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.81 r_work: 0.2786 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21170 Z= 0.154 Angle : 0.548 9.396 28892 Z= 0.273 Chirality : 0.040 0.249 3231 Planarity : 0.004 0.086 3738 Dihedral : 8.344 106.432 3118 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.28 % Favored : 96.25 % Rotamer: Outliers : 3.03 % Allowed : 22.37 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2558 helix: 2.03 (0.15), residues: 1305 sheet: 0.18 (0.34), residues: 242 loop : 0.49 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 403 TYR 0.010 0.001 TYR F 336 PHE 0.014 0.001 PHE B 448 TRP 0.013 0.001 TRP A 364 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (21151) covalent geometry : angle 0.54755 / 0.27 (28890) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 1.20778 / 0.64 ( 2) hydrogen bonds : bond 0.03953 / 2.63 ( 986) hydrogen bonds : angle 4.71763 / 3.39 ( 2769) metal coordination : bond 0.00255 / 0.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.7761 (mpp) cc_final: 0.7462 (mpp) REVERT: A 47 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7341 (mt) REVERT: A 54 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.6103 (m90) REVERT: A 90 ARG cc_start: 0.8119 (mmm160) cc_final: 0.6895 (mmm160) REVERT: A 199 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8066 (pmt170) REVERT: A 300 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9182 (mm) REVERT: A 303 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8778 (pp20) REVERT: A 397 ARG cc_start: 0.6886 (tpp-160) cc_final: 0.5976 (ttp-170) REVERT: B 19 MET cc_start: 0.8412 (pmm) cc_final: 0.8167 (pmm) REVERT: B 39 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7695 (pttt) REVERT: B 53 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6567 (tmm) REVERT: B 350 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8270 (mtt90) REVERT: B 477 LYS cc_start: 0.9294 (mmpt) cc_final: 0.8535 (tttt) REVERT: C 271 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 290 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7959 (ttm170) REVERT: C 418 GLU cc_start: 0.8560 (tt0) cc_final: 0.8310 (tt0) REVERT: C 461 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7600 (m-70) REVERT: C 525 GLN cc_start: 0.8794 (tp40) cc_final: 0.8570 (pp30) REVERT: D 236 ARG cc_start: 0.7755 (ptt90) cc_final: 0.7531 (ppt90) REVERT: D 350 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8215 (mtt90) REVERT: D 383 GLU cc_start: 0.8434 (tt0) cc_final: 0.8058 (tp30) REVERT: D 405 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7781 (mtm180) REVERT: D 501 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 236 ARG cc_start: 0.6990 (ppt170) cc_final: 0.6638 (ppt170) REVERT: E 246 GLN cc_start: 0.8250 (mp10) cc_final: 0.8012 (mp10) REVERT: E 603 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: F 342 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8707 (t0) REVERT: F 403 ARG cc_start: 0.8313 (mmm160) cc_final: 0.8038 (mmm160) REVERT: F 477 LYS cc_start: 0.9366 (tppp) cc_final: 0.9040 (mppt) outliers start: 64 outliers final: 26 residues processed: 207 average time/residue: 0.7135 time to fit residues: 164.9273 Evaluate side-chains 176 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 31 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 214 optimal weight: 0.0770 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN E 234 HIS F 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075686 restraints weight = 36442.426| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.80 r_work: 0.2775 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21170 Z= 0.173 Angle : 0.555 9.426 28892 Z= 0.276 Chirality : 0.041 0.244 3231 Planarity : 0.004 0.093 3738 Dihedral : 8.316 104.964 3118 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.32 % Favored : 96.21 % Rotamer: Outliers : 3.31 % Allowed : 22.37 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.17), residues: 2558 helix: 2.04 (0.15), residues: 1302 sheet: 0.24 (0.34), residues: 241 loop : 0.48 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 403 TYR 0.010 0.001 TYR E 531 PHE 0.018 0.001 PHE A 79 TRP 0.013 0.001 TRP B 364 HIS 0.004 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (21151) covalent geometry : angle 0.55462 / 0.28 (28890) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 1.04757 / 0.55 ( 2) hydrogen bonds : bond 0.04023 / 2.69 ( 986) hydrogen bonds : angle 4.65893 / 3.35 ( 2769) metal coordination : bond 0.00306 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6983 (tpp) cc_final: 0.6691 (tpp) REVERT: A 47 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 54 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6164 (m90) REVERT: A 80 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 90 ARG cc_start: 0.8084 (mmm160) cc_final: 0.6906 (mmm160) REVERT: A 199 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8065 (pmt170) REVERT: A 300 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9176 (mm) REVERT: A 303 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8775 (pp20) REVERT: A 397 ARG cc_start: 0.6930 (tpp-160) cc_final: 0.6001 (ttp-170) REVERT: A 466 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8208 (p0) REVERT: B 19 MET cc_start: 0.8403 (pmm) cc_final: 0.8185 (pmm) REVERT: B 39 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: B 53 MET cc_start: 0.6774 (tmt) cc_final: 0.6531 (tmm) REVERT: B 161 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7555 (mm) REVERT: B 350 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8179 (mtt90) REVERT: B 477 LYS cc_start: 0.9293 (mmpt) cc_final: 0.8547 (tttt) REVERT: C 248 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7910 (tppt) REVERT: C 271 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7254 (tm-30) REVERT: C 418 GLU cc_start: 0.8536 (tt0) cc_final: 0.8255 (tt0) REVERT: C 461 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7616 (m-70) REVERT: C 525 GLN cc_start: 0.8817 (tp40) cc_final: 0.8573 (pp30) REVERT: D 350 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8227 (mtt90) REVERT: D 383 GLU cc_start: 0.8456 (tt0) cc_final: 0.8074 (tp30) REVERT: D 397 ARG cc_start: 0.7476 (pmt-80) cc_final: 0.6679 (pmt-80) REVERT: D 501 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8327 (mm-30) REVERT: E 236 ARG cc_start: 0.6984 (ppt170) cc_final: 0.6638 (ppt170) REVERT: E 246 GLN cc_start: 0.8279 (mp10) cc_final: 0.8020 (mp10) REVERT: E 603 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: F 302 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8847 (mp0) REVERT: F 342 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8691 (t0) REVERT: F 403 ARG cc_start: 0.8368 (mmm160) cc_final: 0.8081 (mmm160) REVERT: F 418 GLU cc_start: 0.8657 (tp30) cc_final: 0.8417 (tp30) REVERT: F 477 LYS cc_start: 0.9381 (tppp) cc_final: 0.9062 (mppt) outliers start: 70 outliers final: 36 residues processed: 206 average time/residue: 0.7139 time to fit residues: 165.3119 Evaluate side-chains 190 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 167 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS ** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN E 234 HIS E 546 ASN F 485 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073297 restraints weight = 36782.171| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.79 r_work: 0.2728 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 21170 Z= 0.297 Angle : 0.619 9.360 28892 Z= 0.309 Chirality : 0.044 0.257 3231 Planarity : 0.005 0.105 3738 Dihedral : 8.393 104.064 3115 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.07 % Favored : 95.54 % Rotamer: Outliers : 3.69 % Allowed : 22.28 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.17), residues: 2558 helix: 1.85 (0.15), residues: 1297 sheet: 0.13 (0.33), residues: 245 loop : 0.37 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 403 TYR 0.015 0.002 TYR B 50 PHE 0.017 0.002 PHE B 448 TRP 0.015 0.002 TRP B 364 HIS 0.007 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.30 (21151) covalent geometry : angle 0.61889 / 0.31 (28890) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.99646 / 0.53 ( 2) hydrogen bonds : bond 0.04901 / 3.29 ( 986) hydrogen bonds : angle 4.84828 / 3.50 ( 2769) metal coordination : bond 0.00543 / 0.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 144 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7464 (mpp) cc_final: 0.7246 (mpp) REVERT: A 40 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6666 (mt) REVERT: A 47 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7402 (mt) REVERT: A 54 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6228 (m90) REVERT: A 63 ARG cc_start: 0.4081 (OUTLIER) cc_final: 0.3505 (pmt-80) REVERT: A 80 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 90 ARG cc_start: 0.8055 (mmm160) cc_final: 0.6891 (mmm160) REVERT: A 199 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8095 (pmt170) REVERT: A 300 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 303 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8743 (pp20) REVERT: A 397 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.5981 (ttm-80) REVERT: A 491 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8050 (mtt-85) REVERT: B 19 MET cc_start: 0.8303 (pmm) cc_final: 0.8031 (pmm) REVERT: B 39 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7738 (pttt) REVERT: B 53 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6516 (tmm) REVERT: B 161 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7587 (mm) REVERT: B 477 LYS cc_start: 0.9315 (mmpt) cc_final: 0.8544 (tttt) REVERT: B 524 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: C 248 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8174 (tppt) REVERT: C 271 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 418 GLU cc_start: 0.8550 (tt0) cc_final: 0.8270 (tt0) REVERT: C 461 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.7606 (m-70) REVERT: C 525 GLN cc_start: 0.8873 (tp40) cc_final: 0.8539 (pp30) REVERT: D 350 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8280 (mtt90) REVERT: D 383 GLU cc_start: 0.8544 (tt0) cc_final: 0.8115 (tp30) REVERT: D 501 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8300 (mm-30) REVERT: E 236 ARG cc_start: 0.7008 (ppt170) cc_final: 0.6653 (ppt170) REVERT: E 246 GLN cc_start: 0.8319 (mp10) cc_final: 0.8058 (mp10) REVERT: E 397 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7235 (tmm-80) REVERT: E 603 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: F 302 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8866 (mp0) REVERT: F 403 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8204 (mmm160) REVERT: F 418 GLU cc_start: 0.8630 (tp30) cc_final: 0.8418 (tp30) REVERT: F 595 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8430 (mtpp) outliers start: 78 outliers final: 38 residues processed: 213 average time/residue: 0.7318 time to fit residues: 174.3765 Evaluate side-chains 194 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 404 SER Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 5 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 220 optimal weight: 0.2980 chunk 239 optimal weight: 0.6980 chunk 222 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076617 restraints weight = 36333.121| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.74 r_work: 0.2799 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21170 Z= 0.121 Angle : 0.551 9.577 28892 Z= 0.273 Chirality : 0.040 0.245 3231 Planarity : 0.004 0.072 3738 Dihedral : 8.184 102.840 3111 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.13 % Favored : 96.52 % Rotamer: Outliers : 2.55 % Allowed : 22.99 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.17), residues: 2558 helix: 2.02 (0.15), residues: 1304 sheet: 0.10 (0.34), residues: 241 loop : 0.45 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 290 TYR 0.010 0.001 TYR F 336 PHE 0.019 0.001 PHE B 448 TRP 0.017 0.001 TRP A 364 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21151) covalent geometry : angle 0.55112 / 0.27 (28890) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.83829 / 0.44 ( 2) hydrogen bonds : bond 0.03643 / 2.43 ( 986) hydrogen bonds : angle 4.56384 / 3.30 ( 2769) metal coordination : bond 0.00262 / 0.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6892 (tpp) cc_final: 0.6500 (tpp) REVERT: A 47 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7493 (mp) REVERT: A 54 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6247 (m-70) REVERT: A 88 LEU cc_start: 0.7298 (tm) cc_final: 0.7035 (tm) REVERT: A 90 ARG cc_start: 0.8016 (mmm160) cc_final: 0.6805 (mmm160) REVERT: A 113 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: A 303 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8735 (pp20) REVERT: A 397 ARG cc_start: 0.6784 (tpp-160) cc_final: 0.5867 (ttp-170) REVERT: A 430 ASP cc_start: 0.8959 (t0) cc_final: 0.8684 (t0) REVERT: B 19 MET cc_start: 0.8288 (pmm) cc_final: 0.8018 (pmm) REVERT: B 39 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7761 (pttt) REVERT: B 53 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6600 (tmm) REVERT: B 350 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8082 (mtt90) REVERT: B 477 LYS cc_start: 0.9261 (mmpt) cc_final: 0.8464 (tttt) REVERT: C 248 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7884 (tppt) REVERT: C 271 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7207 (tm-30) REVERT: C 290 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7782 (ttm170) REVERT: C 418 GLU cc_start: 0.8508 (tt0) cc_final: 0.8197 (tt0) REVERT: C 443 MET cc_start: 0.8175 (mmt) cc_final: 0.7936 (mmt) REVERT: C 461 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7488 (m-70) REVERT: C 525 GLN cc_start: 0.8840 (tp40) cc_final: 0.8572 (pp30) REVERT: D 350 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8168 (mtt90) REVERT: D 383 GLU cc_start: 0.8361 (tt0) cc_final: 0.7906 (tp30) REVERT: D 397 ARG cc_start: 0.7816 (pmt-80) cc_final: 0.7526 (pmt-80) REVERT: D 418 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8001 (mm-30) REVERT: D 501 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 236 ARG cc_start: 0.6948 (ppt170) cc_final: 0.6606 (ppt170) REVERT: E 246 GLN cc_start: 0.8343 (mp10) cc_final: 0.8085 (mp10) REVERT: E 397 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7361 (tmm-80) REVERT: E 603 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: F 342 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8653 (t0) REVERT: F 403 ARG cc_start: 0.8344 (mmm160) cc_final: 0.8047 (mmm160) REVERT: F 418 GLU cc_start: 0.8578 (tp30) cc_final: 0.8290 (tp30) REVERT: F 477 LYS cc_start: 0.9367 (tppp) cc_final: 0.9035 (mppt) REVERT: F 595 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8294 (mtpt) outliers start: 54 outliers final: 26 residues processed: 195 average time/residue: 0.7558 time to fit residues: 164.8429 Evaluate side-chains 180 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 134 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074375 restraints weight = 36589.762| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.81 r_work: 0.2751 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21170 Z= 0.217 Angle : 0.585 9.569 28892 Z= 0.289 Chirality : 0.042 0.223 3231 Planarity : 0.005 0.089 3738 Dihedral : 8.156 102.738 3111 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.79 % Favored : 95.82 % Rotamer: Outliers : 2.37 % Allowed : 23.46 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.17), residues: 2558 helix: 1.96 (0.15), residues: 1299 sheet: -0.00 (0.33), residues: 249 loop : 0.44 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 290 TYR 0.014 0.001 TYR E 310 PHE 0.020 0.001 PHE B 448 TRP 0.014 0.001 TRP B 364 HIS 0.005 0.001 HIS C 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (21151) covalent geometry : angle 0.58513 / 0.29 (28890) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.75624 / 0.40 ( 2) hydrogen bonds : bond 0.04257 / 2.85 ( 986) hydrogen bonds : angle 4.67298 / 3.37 ( 2769) metal coordination : bond 0.00387 / 0.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6864 (tpp) cc_final: 0.6604 (tpp) REVERT: A 47 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7600 (mp) REVERT: A 54 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6187 (m-70) REVERT: A 63 ARG cc_start: 0.4195 (OUTLIER) cc_final: 0.3611 (pmt-80) REVERT: A 88 LEU cc_start: 0.7318 (tm) cc_final: 0.7086 (tm) REVERT: A 90 ARG cc_start: 0.8022 (mmm160) cc_final: 0.6843 (mmm160) REVERT: A 113 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: A 303 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8732 (pp20) REVERT: A 397 ARG cc_start: 0.6985 (tpp-160) cc_final: 0.6020 (ttm-80) REVERT: A 430 ASP cc_start: 0.8982 (t0) cc_final: 0.8745 (t0) REVERT: A 449 GLU cc_start: 0.8660 (mp0) cc_final: 0.7690 (tp30) REVERT: B 19 MET cc_start: 0.8280 (pmm) cc_final: 0.7961 (pmm) REVERT: B 39 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.7759 (pttt) REVERT: B 53 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6543 (tmm) REVERT: B 477 LYS cc_start: 0.9302 (mmpt) cc_final: 0.8563 (tttt) REVERT: C 248 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8114 (tppt) REVERT: C 271 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 418 GLU cc_start: 0.8570 (tt0) cc_final: 0.8262 (tt0) REVERT: C 461 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7686 (m-70) REVERT: C 525 GLN cc_start: 0.8830 (tp40) cc_final: 0.8538 (pp30) REVERT: D 350 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8238 (mtt90) REVERT: D 383 GLU cc_start: 0.8417 (tt0) cc_final: 0.8001 (tp30) REVERT: D 397 ARG cc_start: 0.7856 (pmt-80) cc_final: 0.7560 (pmt-80) REVERT: D 501 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8339 (mm-30) REVERT: E 236 ARG cc_start: 0.6991 (ppt170) cc_final: 0.6640 (ppt170) REVERT: E 397 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7420 (tmm-80) REVERT: E 603 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: F 302 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: F 403 ARG cc_start: 0.8406 (mmm160) cc_final: 0.8110 (mmm160) REVERT: F 477 LYS cc_start: 0.9351 (tppp) cc_final: 0.9041 (mppt) REVERT: F 595 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8427 (mtpp) outliers start: 50 outliers final: 29 residues processed: 187 average time/residue: 0.7287 time to fit residues: 152.3896 Evaluate side-chains 179 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 119 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076679 restraints weight = 36424.933| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.76 r_work: 0.2791 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21170 Z= 0.130 Angle : 0.564 11.773 28892 Z= 0.278 Chirality : 0.040 0.248 3231 Planarity : 0.004 0.082 3738 Dihedral : 8.080 101.680 3111 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.21 % Favored : 96.40 % Rotamer: Outliers : 2.18 % Allowed : 23.60 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.18), residues: 2558 helix: 2.04 (0.15), residues: 1306 sheet: -0.03 (0.33), residues: 249 loop : 0.49 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 290 TYR 0.011 0.001 TYR E 531 PHE 0.021 0.001 PHE B 448 TRP 0.016 0.001 TRP A 364 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21151) covalent geometry : angle 0.56359 / 0.28 (28890) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.75773 / 0.40 ( 2) hydrogen bonds : bond 0.03664 / 2.45 ( 986) hydrogen bonds : angle 4.55528 / 3.29 ( 2769) metal coordination : bond 0.00233 / 0.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7762 (mtm) cc_final: 0.7549 (mpp) REVERT: A 47 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7680 (mp) REVERT: A 54 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6185 (m-70) REVERT: A 88 LEU cc_start: 0.7342 (tm) cc_final: 0.7118 (tm) REVERT: A 90 ARG cc_start: 0.7982 (mmm160) cc_final: 0.6832 (mmm160) REVERT: A 300 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9111 (mm) REVERT: A 303 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8710 (pp20) REVERT: A 397 ARG cc_start: 0.6879 (tpp-160) cc_final: 0.5968 (ttm-80) REVERT: A 430 ASP cc_start: 0.8952 (t0) cc_final: 0.8677 (t0) REVERT: A 449 GLU cc_start: 0.8628 (mp0) cc_final: 0.7549 (tp30) REVERT: B 19 MET cc_start: 0.8306 (pmm) cc_final: 0.7964 (pmm) REVERT: B 53 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6559 (tmm) REVERT: B 350 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8116 (mtt90) REVERT: B 477 LYS cc_start: 0.9269 (mmpt) cc_final: 0.8491 (tttt) REVERT: C 248 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7978 (tppt) REVERT: C 271 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7268 (tm-30) REVERT: C 418 GLU cc_start: 0.8545 (tt0) cc_final: 0.8208 (tt0) REVERT: C 461 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7524 (m-70) REVERT: C 525 GLN cc_start: 0.8848 (tp40) cc_final: 0.8564 (pp30) REVERT: D 350 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8165 (mtt90) REVERT: D 383 GLU cc_start: 0.8352 (tt0) cc_final: 0.7939 (tp30) REVERT: D 397 ARG cc_start: 0.7754 (pmt-80) cc_final: 0.7321 (pmt-80) REVERT: D 501 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 236 ARG cc_start: 0.6967 (ppt170) cc_final: 0.6616 (ppt170) REVERT: E 603 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: F 302 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (mp0) REVERT: F 342 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8664 (t0) REVERT: F 403 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7992 (mmm160) REVERT: F 477 LYS cc_start: 0.9356 (tppp) cc_final: 0.9048 (mppt) REVERT: F 595 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8320 (mtpt) outliers start: 46 outliers final: 24 residues processed: 188 average time/residue: 0.7171 time to fit residues: 151.5343 Evaluate side-chains 176 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 207 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 150 optimal weight: 0.0670 chunk 202 optimal weight: 0.0000 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 chunk 159 optimal weight: 0.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS E 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079047 restraints weight = 36370.422| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.78 r_work: 0.2832 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21170 Z= 0.105 Angle : 0.558 9.851 28892 Z= 0.275 Chirality : 0.039 0.225 3231 Planarity : 0.004 0.072 3738 Dihedral : 7.885 99.946 3107 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.36 % Favored : 96.29 % Rotamer: Outliers : 1.70 % Allowed : 24.12 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2558 helix: 2.18 (0.15), residues: 1306 sheet: -0.00 (0.33), residues: 249 loop : 0.53 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 290 TYR 0.019 0.001 TYR E 356 PHE 0.021 0.001 PHE B 448 TRP 0.017 0.001 TRP C 472 HIS 0.022 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21151) covalent geometry : angle 0.55774 / 0.27 (28890) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.72935 / 0.38 ( 2) hydrogen bonds : bond 0.03128 / 2.07 ( 986) hydrogen bonds : angle 4.41024 / 3.19 ( 2769) metal coordination : bond 0.00182 / 0.08 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6541 (tpp) cc_final: 0.5118 (tmm) REVERT: A 47 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7711 (mt) REVERT: A 54 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6182 (m-70) REVERT: A 63 ARG cc_start: 0.4107 (OUTLIER) cc_final: 0.3610 (pmt-80) REVERT: A 90 ARG cc_start: 0.8017 (mmm160) cc_final: 0.6899 (mmm160) REVERT: A 303 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8716 (pp20) REVERT: A 397 ARG cc_start: 0.6785 (tpp-160) cc_final: 0.5828 (ttm-80) REVERT: A 430 ASP cc_start: 0.8947 (t0) cc_final: 0.8703 (t0) REVERT: A 449 GLU cc_start: 0.8585 (mp0) cc_final: 0.7385 (tp30) REVERT: B 19 MET cc_start: 0.8288 (pmm) cc_final: 0.7957 (pmm) REVERT: B 350 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8075 (mtt90) REVERT: B 477 LYS cc_start: 0.9247 (mmpt) cc_final: 0.8496 (tttt) REVERT: C 248 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7847 (tppt) REVERT: C 271 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7241 (tm-30) REVERT: C 418 GLU cc_start: 0.8528 (tt0) cc_final: 0.8175 (tt0) REVERT: C 443 MET cc_start: 0.8012 (mmt) cc_final: 0.7766 (mmt) REVERT: C 461 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7548 (m-70) REVERT: C 525 GLN cc_start: 0.8804 (tp40) cc_final: 0.8540 (pp30) REVERT: D 383 GLU cc_start: 0.8272 (tt0) cc_final: 0.7925 (tp30) REVERT: D 397 ARG cc_start: 0.7693 (pmt-80) cc_final: 0.7281 (pmt-80) REVERT: D 501 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8297 (mm-30) REVERT: E 236 ARG cc_start: 0.6968 (ppt170) cc_final: 0.6620 (ppt170) REVERT: E 403 ARG cc_start: 0.7291 (mmp80) cc_final: 0.6302 (mpp-170) REVERT: E 603 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: F 342 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8624 (t0) REVERT: F 383 GLU cc_start: 0.8360 (tt0) cc_final: 0.8093 (tm-30) REVERT: F 403 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7828 (mmm160) REVERT: F 477 LYS cc_start: 0.9345 (tppp) cc_final: 0.9017 (mppt) REVERT: F 595 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8278 (mtpt) outliers start: 36 outliers final: 18 residues processed: 186 average time/residue: 0.7277 time to fit residues: 152.6446 Evaluate side-chains 168 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 531 TYR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 214 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 227 optimal weight: 0.0050 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 150 optimal weight: 0.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077984 restraints weight = 36465.957| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.78 r_work: 0.2815 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21170 Z= 0.122 Angle : 0.555 11.865 28892 Z= 0.272 Chirality : 0.040 0.233 3231 Planarity : 0.004 0.069 3738 Dihedral : 7.843 99.335 3107 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.28 % Favored : 96.40 % Rotamer: Outliers : 1.56 % Allowed : 24.27 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.18), residues: 2558 helix: 2.20 (0.15), residues: 1309 sheet: -0.01 (0.34), residues: 234 loop : 0.58 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 290 TYR 0.014 0.001 TYR F 356 PHE 0.020 0.001 PHE A 79 TRP 0.013 0.001 TRP B 364 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (21151) covalent geometry : angle 0.55487 / 0.27 (28890) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.63093 / 0.33 ( 2) hydrogen bonds : bond 0.03342 / 2.23 ( 986) hydrogen bonds : angle 4.41936 / 3.19 ( 2769) metal coordination : bond 0.00220 / 0.11 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6051.83 seconds wall clock time: 104 minutes 14.62 seconds (6254.62 seconds total)