Starting phenix.real_space_refine on Mon May 4 12:55:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ubl_64010/05_2026/9ubl_64010_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ubl_64010/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ubl_64010/05_2026/9ubl_64010_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ubl_64010/05_2026/9ubl_64010_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ubl_64010/05_2026/9ubl_64010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ubl_64010/05_2026/9ubl_64010.map" } 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-2.1rc2-6044/lib/python3.9/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: 4.88, per 1000 atoms: 0.24 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.58 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: 3.60 Time building geometry restraints manager: 2.32 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: 4.970 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.390 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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= 0.270 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 covalent geometry : bond 0.00377 (21151) covalent geometry : angle 0.51895 (28890) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.84154 ( 2) hydrogen bonds : bond 0.15393 ( 986) hydrogen bonds : angle 6.13328 ( 2769) metal coordination : bond 0.00434 ( 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 : 0.955 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: 0.8570 time to fit residues: 253.7116 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 : 0.821 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 31 HIS C 390 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS C 513 ASN D 316 ASN E 234 HIS ** E 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077061 restraints weight = 36332.551| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.76 r_work: 0.2795 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21170 Z= 0.172 Angle : 0.595 9.262 28892 Z= 0.301 Chirality : 0.041 0.236 3231 Planarity : 0.005 0.098 3738 Dihedral : 8.988 106.462 3155 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.21 % Favored : 96.40 % Rotamer: Outliers : 3.69 % Allowed : 21.38 % Favored : 74.93 % 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: 2.05 (0.15), residues: 1305 sheet: 0.11 (0.33), residues: 245 loop : 0.50 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 403 TYR 0.017 0.001 TYR B 50 PHE 0.013 0.001 PHE B 448 TRP 0.014 0.001 TRP B 364 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00396 (21151) covalent geometry : angle 0.59476 (28890) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.46890 ( 2) hydrogen bonds : bond 0.04590 ( 986) hydrogen bonds : angle 5.00066 ( 2769) metal coordination : bond 0.00243 ( 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 241 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 54 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.5925 (m90) REVERT: A 86 TRP cc_start: 0.9026 (t60) cc_final: 0.8452 (t60) REVERT: A 90 ARG cc_start: 0.8152 (mmm160) cc_final: 0.6936 (mmm160) REVERT: A 300 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9162 (mm) REVERT: A 303 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8807 (pp20) REVERT: A 397 ARG cc_start: 0.6836 (tpp-160) cc_final: 0.5918 (ttp-170) REVERT: B 33 LEU cc_start: 0.6462 (mm) cc_final: 0.6122 (mm) REVERT: B 39 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7703 (pttt) REVERT: B 53 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6518 (tmm) REVERT: B 350 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8553 (mtt90) REVERT: B 477 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8450 (tttt) REVERT: B 491 ARG cc_start: 0.8778 (mtp-110) cc_final: 0.8134 (mtt-85) REVERT: C 290 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7854 (ttm170) REVERT: C 461 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7468 (m-70) REVERT: C 525 GLN cc_start: 0.8826 (tp40) cc_final: 0.8590 (pp30) REVERT: D 383 GLU cc_start: 0.8463 (tt0) cc_final: 0.8043 (tp30) REVERT: D 397 ARG cc_start: 0.7395 (pmt-80) cc_final: 0.7004 (pmt-80) REVERT: D 403 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7531 (mtm110) REVERT: D 501 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 236 ARG cc_start: 0.6916 (ppt170) cc_final: 0.6493 (ppt170) REVERT: E 246 GLN cc_start: 0.8289 (mp10) cc_final: 0.8042 (mp10) REVERT: E 383 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8072 (tm-30) REVERT: E 603 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: F 342 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8635 (t0) outliers start: 78 outliers final: 26 residues processed: 228 average time/residue: 0.7529 time to fit residues: 191.3184 Evaluate side-chains 178 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 6 CYS Chi-restraints excluded: chain B residue 14 VAL 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 246 GLN 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: 1.9990 chunk 47 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS ** E 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076847 restraints weight = 36416.358| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.76 r_work: 0.2795 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21170 Z= 0.145 Angle : 0.546 9.884 28892 Z= 0.274 Chirality : 0.040 0.239 3231 Planarity : 0.004 0.089 3738 Dihedral : 8.493 106.458 3124 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.36 % Favored : 96.25 % Rotamer: Outliers : 3.26 % Allowed : 21.85 % Favored : 74.88 % 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: 1.85 (0.17), residues: 2558 helix: 2.07 (0.15), residues: 1308 sheet: 0.14 (0.34), residues: 242 loop : 0.49 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 403 TYR 0.011 0.001 TYR E 356 PHE 0.018 0.001 PHE A 79 TRP 0.013 0.001 TRP B 364 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00337 (21151) covalent geometry : angle 0.54643 (28890) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.13918 ( 2) hydrogen bonds : bond 0.04010 ( 986) hydrogen bonds : angle 4.73445 ( 2769) metal coordination : bond 0.00238 ( 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 221 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.7818 (mpp) cc_final: 0.7521 (mpp) REVERT: A 47 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7364 (mt) REVERT: A 54 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6088 (m90) REVERT: A 90 ARG cc_start: 0.8114 (mmm160) cc_final: 0.6888 (mmm160) REVERT: A 199 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8027 (pmt170) REVERT: A 300 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9147 (mm) REVERT: A 303 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8782 (pp20) REVERT: A 397 ARG cc_start: 0.6812 (tpp-160) cc_final: 0.5900 (ttp-170) REVERT: A 466 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8220 (p0) REVERT: B 33 LEU cc_start: 0.5562 (mm) cc_final: 0.5326 (mm) REVERT: B 39 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7718 (pttt) REVERT: B 53 MET cc_start: 0.6811 (tmt) cc_final: 0.6557 (tmm) REVERT: B 477 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8448 (tttt) REVERT: C 271 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 290 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7898 (ttm170) REVERT: C 418 GLU cc_start: 0.8523 (tt0) cc_final: 0.8002 (pt0) REVERT: C 461 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7494 (m-70) REVERT: C 525 GLN cc_start: 0.8848 (tp40) cc_final: 0.8580 (pp30) REVERT: D 350 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8160 (mtt90) REVERT: D 383 GLU cc_start: 0.8392 (tt0) cc_final: 0.8001 (tp30) REVERT: D 397 ARG cc_start: 0.7433 (pmt-80) cc_final: 0.7221 (pmt-80) REVERT: D 418 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8092 (tp30) REVERT: D 501 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 236 ARG cc_start: 0.6930 (ppt170) cc_final: 0.6558 (ppt170) REVERT: E 246 GLN cc_start: 0.8326 (mp10) cc_final: 0.8071 (mp10) REVERT: E 383 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 397 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7479 (tmm-80) REVERT: E 418 GLU cc_start: 0.8251 (tp30) cc_final: 0.8005 (tp30) REVERT: E 603 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: F 342 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8681 (t0) REVERT: F 403 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8044 (mmm160) REVERT: F 477 LYS cc_start: 0.9375 (tppp) cc_final: 0.9056 (mppt) REVERT: F 524 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8265 (tp30) outliers start: 69 outliers final: 26 residues processed: 213 average time/residue: 0.7829 time to fit residues: 185.2308 Evaluate side-chains 179 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 466 ASP Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 LYS 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 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 243 ASP Chi-restraints excluded: chain C residue 246 GLN 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 397 ARG 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 524 GLU 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: 0.5980 chunk 204 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 372 ASN D 316 ASN E 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075908 restraints weight = 36715.562| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.81 r_work: 0.2777 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1871 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= 0.157 Angle : 0.539 9.544 28892 Z= 0.269 Chirality : 0.040 0.241 3231 Planarity : 0.004 0.094 3738 Dihedral : 8.220 103.554 3114 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.40 % Favored : 96.17 % Rotamer: Outliers : 3.07 % Allowed : 22.52 % Favored : 74.41 % 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: 1.87 (0.18), residues: 2558 helix: 2.09 (0.15), residues: 1303 sheet: 0.12 (0.34), residues: 249 loop : 0.53 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 403 TYR 0.011 0.001 TYR F 336 PHE 0.014 0.001 PHE B 448 TRP 0.013 0.001 TRP B 364 HIS 0.004 0.001 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00367 (21151) covalent geometry : angle 0.53943 (28890) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.83491 ( 2) hydrogen bonds : bond 0.03893 ( 986) hydrogen bonds : angle 4.61321 ( 2769) metal coordination : bond 0.00300 ( 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 218 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6887 (tpp) cc_final: 0.6582 (tpp) REVERT: A 19 MET cc_start: 0.7735 (mpp) cc_final: 0.7517 (mpp) REVERT: A 54 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6106 (m-70) REVERT: A 90 ARG cc_start: 0.8066 (mmm160) cc_final: 0.6832 (mmm160) REVERT: A 300 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9167 (mm) REVERT: A 303 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8752 (pp20) REVERT: A 397 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6087 (ttp-170) REVERT: A 466 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8163 (p0) REVERT: B 39 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7734 (pttt) REVERT: B 53 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6625 (tmm) REVERT: B 350 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8761 (mtt90) REVERT: B 477 LYS cc_start: 0.9296 (mmpt) cc_final: 0.8547 (tttt) REVERT: B 573 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7691 (mtt90) REVERT: C 248 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7931 (tppt) REVERT: C 271 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7134 (tm-30) REVERT: C 418 GLU cc_start: 0.8579 (tt0) cc_final: 0.8277 (tt0) REVERT: C 461 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: C 525 GLN cc_start: 0.8847 (tp40) cc_final: 0.8609 (pp30) REVERT: C 578 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8651 (mtpp) REVERT: D 350 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8207 (mtt90) REVERT: D 383 GLU cc_start: 0.8446 (tt0) cc_final: 0.8069 (tp30) REVERT: D 397 ARG cc_start: 0.7659 (pmt-80) cc_final: 0.7307 (pmt-80) REVERT: D 501 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 236 ARG cc_start: 0.7004 (ppt170) cc_final: 0.6636 (ppt170) REVERT: E 246 GLN cc_start: 0.8319 (mp10) cc_final: 0.8045 (mp10) REVERT: E 383 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8179 (tm-30) REVERT: E 397 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7574 (tmm-80) REVERT: E 418 GLU cc_start: 0.8315 (tp30) cc_final: 0.8039 (tp30) REVERT: E 603 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: F 302 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: F 342 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8681 (t0) REVERT: F 403 ARG cc_start: 0.8366 (mmm160) cc_final: 0.8113 (mmm160) REVERT: F 418 GLU cc_start: 0.8615 (tp30) cc_final: 0.8344 (tp30) REVERT: F 477 LYS cc_start: 0.9423 (tppp) cc_final: 0.9118 (mppt) REVERT: F 524 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: F 595 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8381 (mtpp) outliers start: 65 outliers final: 27 residues processed: 211 average time/residue: 0.7508 time to fit residues: 176.7787 Evaluate side-chains 185 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 466 ASP 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 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 459 THR Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain C residue 243 ASP 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 591 GLN 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 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 606 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 31 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 173 optimal weight: 0.0000 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3552 r_free = 0.3552 target = 0.108719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075561 restraints weight = 36548.929| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.75 r_work: 0.2781 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21170 Z= 0.169 Angle : 0.541 9.701 28892 Z= 0.269 Chirality : 0.041 0.243 3231 Planarity : 0.004 0.072 3738 Dihedral : 8.094 102.698 3111 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.44 % Favored : 96.09 % Rotamer: Outliers : 3.55 % Allowed : 22.33 % Favored : 74.12 % 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: 1.85 (0.17), residues: 2558 helix: 2.09 (0.15), residues: 1299 sheet: 0.10 (0.34), residues: 249 loop : 0.50 (0.21), residues: 1010 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 0.017 0.001 PHE A 79 TRP 0.014 0.001 TRP A 364 HIS 0.004 0.001 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00399 (21151) covalent geometry : angle 0.54123 (28890) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.79988 ( 2) hydrogen bonds : bond 0.03926 ( 986) hydrogen bonds : angle 4.58689 ( 2769) metal coordination : bond 0.00320 ( 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 224 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7729 (mpp) cc_final: 0.7434 (mpp) REVERT: A 47 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 54 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6164 (m90) REVERT: A 63 ARG cc_start: 0.3969 (OUTLIER) cc_final: 0.3411 (pmt-80) REVERT: A 80 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 88 LEU cc_start: 0.7275 (tm) cc_final: 0.7004 (tm) REVERT: A 90 ARG cc_start: 0.8030 (mmm160) cc_final: 0.6829 (mmm160) REVERT: A 199 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8016 (pmt170) REVERT: A 300 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9108 (mm) REVERT: A 303 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8734 (pp20) REVERT: A 397 ARG cc_start: 0.7007 (tpp-160) cc_final: 0.5940 (ttm-80) REVERT: A 430 ASP cc_start: 0.8936 (t0) cc_final: 0.8690 (t0) REVERT: A 466 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8188 (p0) REVERT: B 39 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7775 (pttt) REVERT: B 53 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6517 (tmm) REVERT: B 161 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 477 LYS cc_start: 0.9249 (mmpt) cc_final: 0.8471 (tttt) REVERT: B 573 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7584 (mtt90) REVERT: C 248 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7927 (tppt) REVERT: C 271 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7128 (tm-30) REVERT: C 418 GLU cc_start: 0.8495 (tt0) cc_final: 0.8163 (tt0) REVERT: C 443 MET cc_start: 0.8159 (mmt) cc_final: 0.7921 (mmt) REVERT: C 461 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7479 (m-70) REVERT: C 525 GLN cc_start: 0.8866 (tp40) cc_final: 0.8558 (pp30) REVERT: C 578 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8494 (mtpp) REVERT: D 350 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8161 (mtt90) REVERT: D 383 GLU cc_start: 0.8346 (tt0) cc_final: 0.7921 (tp30) REVERT: D 501 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8277 (mm-30) REVERT: E 236 ARG cc_start: 0.6971 (ppt170) cc_final: 0.6612 (ppt170) REVERT: E 246 GLN cc_start: 0.8343 (mp10) cc_final: 0.8107 (mp10) REVERT: E 383 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 397 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7510 (tmm-80) REVERT: E 418 GLU cc_start: 0.8293 (tp30) cc_final: 0.8029 (tp30) REVERT: E 603 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: F 302 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: F 342 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8644 (t0) REVERT: F 403 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8127 (mmm160) REVERT: F 418 GLU cc_start: 0.8555 (tp30) cc_final: 0.8249 (tp30) REVERT: F 477 LYS cc_start: 0.9362 (tppp) cc_final: 0.9125 (tppt) REVERT: F 524 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: F 595 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8305 (mtpp) outliers start: 75 outliers final: 32 residues processed: 215 average time/residue: 0.7629 time to fit residues: 183.1074 Evaluate side-chains 194 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 311 MET 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 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 544 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain C residue 243 ASP 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 387 CYS 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 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 302 GLU Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 524 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 167 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 554 GLN E 234 HIS E 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074537 restraints weight = 36607.484| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.76 r_work: 0.2759 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21170 Z= 0.206 Angle : 0.562 9.543 28892 Z= 0.280 Chirality : 0.042 0.248 3231 Planarity : 0.004 0.090 3738 Dihedral : 8.120 101.955 3111 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.79 % Favored : 95.78 % Rotamer: Outliers : 3.41 % Allowed : 22.47 % Favored : 74.12 % 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: 1.78 (0.17), residues: 2558 helix: 2.04 (0.15), residues: 1299 sheet: 0.05 (0.33), residues: 249 loop : 0.46 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 403 TYR 0.013 0.001 TYR E 310 PHE 0.017 0.001 PHE B 448 TRP 0.015 0.001 TRP A 364 HIS 0.005 0.001 HIS C 461 Details of bonding type rmsd covalent geometry : bond 0.00488 (21151) covalent geometry : angle 0.56203 (28890) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.74825 ( 2) hydrogen bonds : bond 0.04195 ( 986) hydrogen bonds : angle 4.62453 ( 2769) metal coordination : bond 0.00393 ( 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 226 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 154 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7702 (mpp) cc_final: 0.7457 (mpp) REVERT: A 47 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 54 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6251 (m-70) REVERT: A 63 ARG cc_start: 0.4011 (OUTLIER) cc_final: 0.3482 (pmt-80) REVERT: A 90 ARG cc_start: 0.8011 (mmm160) cc_final: 0.6890 (mmm160) REVERT: A 300 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 397 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6103 (ttp-170) REVERT: A 430 ASP cc_start: 0.8925 (t0) cc_final: 0.8667 (t0) REVERT: A 466 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8196 (p0) REVERT: B 53 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6538 (tmm) REVERT: B 350 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8708 (mtt90) REVERT: B 477 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8485 (tttt) REVERT: C 248 LYS cc_start: 0.8318 (ttpp) cc_final: 0.8028 (tppt) REVERT: C 254 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 271 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7201 (tm-30) REVERT: C 418 GLU cc_start: 0.8482 (tt0) cc_final: 0.8163 (tt0) REVERT: C 461 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7521 (m-70) REVERT: C 525 GLN cc_start: 0.8872 (tp40) cc_final: 0.8529 (pp30) REVERT: C 578 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8520 (mtpp) REVERT: D 350 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8179 (mtt90) REVERT: D 383 GLU cc_start: 0.8359 (tt0) cc_final: 0.7938 (tp30) REVERT: D 397 ARG cc_start: 0.7703 (pmt-80) cc_final: 0.7288 (pmt-80) REVERT: D 501 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 236 ARG cc_start: 0.6979 (ppt170) cc_final: 0.6612 (ppt170) REVERT: E 246 GLN cc_start: 0.8368 (mp10) cc_final: 0.8126 (mp10) REVERT: E 383 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8163 (tm-30) REVERT: E 397 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7476 (tmm-80) REVERT: E 418 GLU cc_start: 0.8353 (tp30) cc_final: 0.8099 (tp30) REVERT: E 430 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8538 (t0) REVERT: E 603 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7067 (mp10) REVERT: F 302 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8851 (mp0) REVERT: F 342 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8664 (t0) REVERT: F 403 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8176 (mmm160) REVERT: F 418 GLU cc_start: 0.8543 (tp30) cc_final: 0.8207 (tp30) REVERT: F 477 LYS cc_start: 0.9357 (tppp) cc_final: 0.9121 (tppt) REVERT: F 524 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: F 595 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8340 (mtpp) outliers start: 72 outliers final: 35 residues processed: 217 average time/residue: 0.7497 time to fit residues: 181.9406 Evaluate side-chains 194 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 300 ILE Chi-restraints excluded: chain A residue 303 GLU 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 53 MET Chi-restraints excluded: chain B residue 93 GLN 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 243 ASP Chi-restraints excluded: chain C residue 254 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 C residue 577 LEU Chi-restraints excluded: chain D residue 313 LEU 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 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 430 ASP 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 524 GLU 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: 20.0000 chunk 224 optimal weight: 0.0370 chunk 220 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 231 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** 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 = 0.3573 r_free = 0.3573 target = 0.110361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077285 restraints weight = 36400.992| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.77 r_work: 0.2814 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21170 Z= 0.109 Angle : 0.534 9.704 28892 Z= 0.263 Chirality : 0.039 0.243 3231 Planarity : 0.004 0.066 3738 Dihedral : 7.917 100.221 3106 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.32 % Favored : 96.33 % Rotamer: Outliers : 2.41 % Allowed : 23.37 % 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: 1.94 (0.18), residues: 2558 helix: 2.19 (0.15), residues: 1305 sheet: -0.02 (0.33), residues: 250 loop : 0.55 (0.22), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 290 TYR 0.009 0.001 TYR F 336 PHE 0.019 0.001 PHE B 448 TRP 0.014 0.001 TRP A 364 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00248 (21151) covalent geometry : angle 0.53388 (28890) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.60321 ( 2) hydrogen bonds : bond 0.03335 ( 986) hydrogen bonds : angle 4.41097 ( 2769) metal coordination : bond 0.00162 ( 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 211 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6747 (tpp) cc_final: 0.6402 (tpp) REVERT: A 19 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: A 47 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 54 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6158 (m-70) REVERT: A 63 ARG cc_start: 0.3995 (OUTLIER) cc_final: 0.3449 (pmt-80) REVERT: A 88 LEU cc_start: 0.7303 (tm) cc_final: 0.7025 (tm) REVERT: A 90 ARG cc_start: 0.7992 (mmm160) cc_final: 0.6906 (mmm160) REVERT: A 303 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8695 (pp20) REVERT: A 397 ARG cc_start: 0.7099 (tpp-160) cc_final: 0.6037 (ttm-80) REVERT: A 430 ASP cc_start: 0.8909 (t0) cc_final: 0.8658 (t0) REVERT: A 449 GLU cc_start: 0.8682 (mp0) cc_final: 0.7498 (tp30) REVERT: A 466 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 53 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6599 (tmm) REVERT: B 477 LYS cc_start: 0.9255 (mmpt) cc_final: 0.8490 (tttt) REVERT: C 248 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7864 (tppt) REVERT: C 271 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7150 (tm-30) REVERT: C 418 GLU cc_start: 0.8479 (tt0) cc_final: 0.8146 (tt0) REVERT: C 461 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7486 (m-70) REVERT: C 525 GLN cc_start: 0.8849 (tp40) cc_final: 0.8580 (pp30) REVERT: D 350 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8118 (mtt90) REVERT: D 383 GLU cc_start: 0.8325 (tt0) cc_final: 0.7960 (tp30) REVERT: D 397 ARG cc_start: 0.7622 (pmt-80) cc_final: 0.7200 (pmt-80) REVERT: D 501 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8346 (mm-30) REVERT: E 236 ARG cc_start: 0.7037 (ppt170) cc_final: 0.6682 (ppt170) REVERT: E 246 GLN cc_start: 0.8297 (mp10) cc_final: 0.8069 (mp10) REVERT: E 383 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8148 (tm-30) REVERT: E 397 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (tmm-80) REVERT: E 418 GLU cc_start: 0.8276 (tp30) cc_final: 0.8010 (tp30) REVERT: E 603 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: F 342 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8622 (t0) REVERT: F 403 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8100 (mmm160) REVERT: F 418 GLU cc_start: 0.8560 (tp30) cc_final: 0.8212 (tp30) REVERT: F 477 LYS cc_start: 0.9349 (tppp) cc_final: 0.9032 (mppt) REVERT: F 595 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8281 (mtpt) outliers start: 51 outliers final: 20 residues processed: 202 average time/residue: 0.7778 time to fit residues: 174.7201 Evaluate side-chains 180 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 303 GLU 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 53 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 243 ASP 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 606 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 134 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075862 restraints weight = 36652.383| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.79 r_work: 0.2776 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21170 Z= 0.179 Angle : 0.553 9.788 28892 Z= 0.273 Chirality : 0.041 0.204 3231 Planarity : 0.004 0.071 3738 Dihedral : 7.941 99.973 3106 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.83 % Favored : 95.78 % Rotamer: Outliers : 2.51 % Allowed : 23.27 % 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: 1.89 (0.18), residues: 2558 helix: 2.13 (0.15), residues: 1303 sheet: -0.02 (0.33), residues: 250 loop : 0.54 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 290 TYR 0.011 0.001 TYR F 356 PHE 0.019 0.001 PHE B 448 TRP 0.013 0.001 TRP A 364 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00426 (21151) covalent geometry : angle 0.55272 (28890) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.54344 ( 2) hydrogen bonds : bond 0.03899 ( 986) hydrogen bonds : angle 4.51115 ( 2769) metal coordination : bond 0.00353 ( 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 198 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7401 (mpp) REVERT: A 47 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7665 (mp) REVERT: A 54 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6681 (m90) REVERT: A 63 ARG cc_start: 0.4144 (OUTLIER) cc_final: 0.3599 (pmt-80) REVERT: A 88 LEU cc_start: 0.7323 (tm) cc_final: 0.7045 (tm) REVERT: A 90 ARG cc_start: 0.7954 (mmm160) cc_final: 0.6908 (mmm160) REVERT: A 397 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6142 (ttp-170) REVERT: A 430 ASP cc_start: 0.8940 (t0) cc_final: 0.8692 (t0) REVERT: A 466 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8181 (p0) REVERT: B 93 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8903 (mp10) REVERT: B 477 LYS cc_start: 0.9269 (mmpt) cc_final: 0.8505 (tttt) REVERT: C 248 LYS cc_start: 0.8312 (ttpp) cc_final: 0.8015 (tppt) REVERT: C 271 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 290 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7805 (ttm170) REVERT: C 418 GLU cc_start: 0.8507 (tt0) cc_final: 0.8166 (tt0) REVERT: C 461 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: C 525 GLN cc_start: 0.8859 (tp40) cc_final: 0.8535 (pp30) REVERT: D 350 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8175 (mtt90) REVERT: D 383 GLU cc_start: 0.8361 (tt0) cc_final: 0.8007 (tp30) REVERT: D 501 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8283 (mm-30) REVERT: E 236 ARG cc_start: 0.6997 (ppt170) cc_final: 0.6647 (ppt170) REVERT: E 246 GLN cc_start: 0.8302 (mp10) cc_final: 0.8084 (mp10) REVERT: E 383 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8140 (tm-30) REVERT: E 397 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7427 (tmm-80) REVERT: E 418 GLU cc_start: 0.8297 (tp30) cc_final: 0.8048 (tp30) REVERT: E 603 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: F 342 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8679 (t0) REVERT: F 403 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8113 (mmm160) REVERT: F 418 GLU cc_start: 0.8607 (tp30) cc_final: 0.8284 (tp30) REVERT: F 477 LYS cc_start: 0.9356 (tppp) cc_final: 0.9030 (mppt) REVERT: F 524 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: F 595 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8351 (mtpp) outliers start: 53 outliers final: 26 residues processed: 187 average time/residue: 0.7409 time to fit residues: 155.2622 Evaluate side-chains 181 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 466 ASP Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 384 ASP 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 243 ASP 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 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 342 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 524 GLU 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: 0.9990 chunk 120 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 209 optimal weight: 0.9990 chunk 200 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 178 optimal weight: 0.2980 chunk 166 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3583 r_free = 0.3583 target = 0.111247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078022 restraints weight = 36414.462| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.80 r_work: 0.2816 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21170 Z= 0.105 Angle : 0.533 10.270 28892 Z= 0.261 Chirality : 0.039 0.207 3231 Planarity : 0.004 0.057 3738 Dihedral : 7.850 98.407 3106 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.48 % Rotamer: Outliers : 1.89 % Allowed : 23.89 % 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: 2.00 (0.18), residues: 2558 helix: 2.25 (0.15), residues: 1308 sheet: -0.03 (0.33), residues: 250 loop : 0.57 (0.22), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 403 TYR 0.010 0.001 TYR E 531 PHE 0.019 0.001 PHE B 448 TRP 0.014 0.001 TRP C 472 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00234 (21151) covalent geometry : angle 0.53297 (28890) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.44442 ( 2) hydrogen bonds : bond 0.03222 ( 986) hydrogen bonds : angle 4.35440 ( 2769) metal coordination : bond 0.00159 ( 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 190 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6556 (tpp) cc_final: 0.5085 (tmm) REVERT: A 19 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: A 47 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 54 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6272 (m-70) REVERT: A 63 ARG cc_start: 0.4039 (OUTLIER) cc_final: 0.3561 (pmt-80) REVERT: A 88 LEU cc_start: 0.7350 (tm) cc_final: 0.7111 (tm) REVERT: A 90 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7032 (mmm160) REVERT: A 300 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9113 (mm) REVERT: A 397 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.6098 (ttp-170) REVERT: A 430 ASP cc_start: 0.8935 (t0) cc_final: 0.8686 (t0) REVERT: A 449 GLU cc_start: 0.8625 (mp0) cc_final: 0.7499 (tp30) REVERT: A 466 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8122 (p0) REVERT: B 477 LYS cc_start: 0.9267 (mmpt) cc_final: 0.8528 (tttt) REVERT: C 271 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 290 ARG cc_start: 0.8383 (mtp85) cc_final: 0.7848 (ttm170) REVERT: C 418 GLU cc_start: 0.8503 (tt0) cc_final: 0.8149 (tt0) REVERT: C 461 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7678 (m-70) REVERT: C 525 GLN cc_start: 0.8832 (tp40) cc_final: 0.8565 (pp30) REVERT: D 350 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8126 (mtt90) REVERT: D 383 GLU cc_start: 0.8315 (tt0) cc_final: 0.7972 (tp30) REVERT: D 397 ARG cc_start: 0.7640 (pmt-80) cc_final: 0.7199 (pmt-80) REVERT: D 501 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 236 ARG cc_start: 0.7057 (ppt170) cc_final: 0.6705 (ppt170) REVERT: E 246 GLN cc_start: 0.8279 (mp10) cc_final: 0.8060 (mp10) REVERT: E 383 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8184 (tm-30) REVERT: E 397 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7341 (tmm-80) REVERT: E 603 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: F 342 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8650 (t0) REVERT: F 383 GLU cc_start: 0.8407 (tt0) cc_final: 0.8143 (tm-30) REVERT: F 418 GLU cc_start: 0.8582 (tp30) cc_final: 0.8242 (tp30) REVERT: F 477 LYS cc_start: 0.9353 (tppp) cc_final: 0.9050 (mppt) REVERT: F 524 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: F 595 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8312 (mtpt) outliers start: 40 outliers final: 19 residues processed: 184 average time/residue: 0.7462 time to fit residues: 154.1466 Evaluate side-chains 176 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 300 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 243 ASP 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 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 524 GLU 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: 0.9990 chunk 79 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 202 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 159 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3591 r_free = 0.3591 target = 0.111749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078551 restraints weight = 36415.427| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.81 r_work: 0.2824 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21170 Z= 0.107 Angle : 0.536 9.956 28892 Z= 0.262 Chirality : 0.039 0.232 3231 Planarity : 0.004 0.050 3738 Dihedral : 7.785 97.205 3106 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.44 % Favored : 96.25 % Rotamer: Outliers : 1.66 % Allowed : 24.08 % Favored : 74.27 % 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: 2.06 (0.18), residues: 2558 helix: 2.30 (0.15), residues: 1302 sheet: 0.00 (0.34), residues: 239 loop : 0.59 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.016 0.001 TYR F 356 PHE 0.020 0.001 PHE B 448 TRP 0.014 0.001 TRP A 86 HIS 0.009 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00242 (21151) covalent geometry : angle 0.53622 (28890) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.37954 ( 2) hydrogen bonds : bond 0.03171 ( 986) hydrogen bonds : angle 4.31853 ( 2769) metal coordination : bond 0.00197 ( 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 184 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6726 (tpp) cc_final: 0.5356 (tmm) REVERT: A 19 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: A 47 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 54 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6219 (m-70) REVERT: A 63 ARG cc_start: 0.3982 (OUTLIER) cc_final: 0.3495 (pmt-80) REVERT: A 88 LEU cc_start: 0.7339 (tm) cc_final: 0.7101 (tm) REVERT: A 90 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7073 (mmm160) REVERT: A 300 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 397 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6217 (ttp-170) REVERT: A 430 ASP cc_start: 0.8957 (t0) cc_final: 0.8747 (t0) REVERT: A 449 GLU cc_start: 0.8626 (mp0) cc_final: 0.7577 (tp30) REVERT: A 466 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 477 LYS cc_start: 0.9267 (mmpt) cc_final: 0.8533 (tttt) REVERT: C 271 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 275 LYS cc_start: 0.8847 (mtpm) cc_final: 0.8617 (mtpp) REVERT: C 418 GLU cc_start: 0.8508 (tt0) cc_final: 0.8138 (tt0) REVERT: C 461 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7682 (m-70) REVERT: C 525 GLN cc_start: 0.8829 (tp40) cc_final: 0.8562 (pp30) REVERT: D 350 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8125 (mtt90) REVERT: D 383 GLU cc_start: 0.8302 (tt0) cc_final: 0.7991 (tp30) REVERT: D 397 ARG cc_start: 0.7642 (pmt-80) cc_final: 0.7241 (pmt-80) REVERT: D 501 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8317 (mm-30) REVERT: E 236 ARG cc_start: 0.7059 (ppt170) cc_final: 0.6704 (ppt170) REVERT: E 603 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: F 342 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8593 (t0) REVERT: F 383 GLU cc_start: 0.8407 (tt0) cc_final: 0.8156 (tm-30) REVERT: F 418 GLU cc_start: 0.8572 (tp30) cc_final: 0.8242 (tp30) REVERT: F 477 LYS cc_start: 0.9340 (tppp) cc_final: 0.9036 (mppt) REVERT: F 524 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: F 595 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8312 (mtpt) outliers start: 35 outliers final: 17 residues processed: 181 average time/residue: 0.7066 time to fit residues: 143.8949 Evaluate side-chains 172 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET 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 300 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 461 HIS 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 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 524 GLU 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 214 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 227 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 150 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 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 = 0.3600 r_free = 0.3600 target = 0.112517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079318 restraints weight = 36475.576| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.82 r_work: 0.2836 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21170 Z= 0.102 Angle : 0.536 12.701 28892 Z= 0.259 Chirality : 0.039 0.228 3231 Planarity : 0.004 0.057 3738 Dihedral : 7.708 96.461 3106 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.24 % Favored : 96.44 % Rotamer: Outliers : 1.56 % Allowed : 24.22 % 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: 2.11 (0.18), residues: 2558 helix: 2.34 (0.15), residues: 1302 sheet: 0.03 (0.34), residues: 234 loop : 0.62 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 290 TYR 0.009 0.001 TYR E 531 PHE 0.021 0.001 PHE A 79 TRP 0.013 0.001 TRP C 472 HIS 0.006 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00230 (21151) covalent geometry : angle 0.53627 (28890) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.43928 ( 2) hydrogen bonds : bond 0.03043 ( 986) hydrogen bonds : angle 4.26578 ( 2769) metal coordination : bond 0.00185 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6031.73 seconds wall clock time: 104 minutes 4.43 seconds (6244.43 seconds total)