Starting phenix.real_space_refine on Fri Aug 7 15:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1g_65536/08_2026/9w1g_65536_neut_trim.cif" } resolution = 2.89 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= 0.002 sd= 0.032 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 84 5.16 5 C 13653 2.51 5 N 3971 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21716 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4690 Classifications: {'peptide': 599} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 557} Chain breaks: 1 Chain: "B" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4610 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 547} Chain breaks: 2 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': 5, 'rna3p_pur': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} 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: 5.67, per 1000 atoms: 0.26 Number of scatterers: 21716 At special positions: 0 Unit cell: (96.928, 126.752, 179.876, 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 84 16.00 P 24 15.00 Mg 6 11.99 O 3972 8.00 N 3971 7.00 C 13653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 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 262 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 461 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 260 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 461 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 262 " 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 260 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 461 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 260 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 461 " 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 9 sheets defined 54.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.587A pdb=" N VAL A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 3.596A pdb=" N HIS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 143 through 153 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.842A pdb=" N ARG A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.759A pdb=" N GLU A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) 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: 3.798A pdb=" N ARG A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.195A 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: 3.945A 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 19 Processing helix chain 'B' and resid 20 through 21 No H-bonds generated for 'chain 'B' and resid 20 through 21' Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.550A pdb=" N GLY B 26 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 removed outlier: 3.594A pdb=" N GLN B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.860A pdb=" N HIS B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.596A pdb=" N GLU B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (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: 3.619A 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 306 through 313 Processing helix chain 'B' and resid 324 through 342 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 removed outlier: 3.563A pdb=" N HIS B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.989A 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: 3.654A pdb=" N THR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.702A pdb=" N ALA C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.564A pdb=" N GLU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 314 removed outlier: 4.287A pdb=" N ARG C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 342 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: 3.651A pdb=" N GLU C 399 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 3.856A pdb=" N ARG C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 removed outlier: 3.946A 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 477 Processing helix chain 'C' and resid 488 through 491 removed outlier: 3.660A 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 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 removed outlier: 3.548A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 305 through 314 removed outlier: 4.167A pdb=" N ARG D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 323 removed outlier: 3.874A 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 342 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: 3.663A 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: 3.586A 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: 3.705A 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: 4.074A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.629A 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 306 through 314 removed outlier: 4.316A pdb=" N GLY E 314 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 323 removed outlier: 3.779A 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 342 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: 3.945A pdb=" N ALA E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 removed outlier: 4.000A 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 removed outlier: 3.537A pdb=" N VAL E 454 " --> pdb=" O PRO E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 488 through 491 removed outlier: 3.725A pdb=" N ARG E 491 " --> pdb=" O HIS E 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 492 through 502 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 540 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.111A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 3.949A 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 224 through 230 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 246 through 253 removed outlier: 4.312A pdb=" N TRP F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.857A 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 314 removed outlier: 3.567A pdb=" N GLY F 314 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.965A 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 362 through 381 Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.983A pdb=" N GLU F 399 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 420 removed outlier: 3.622A pdb=" N ARG F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 435 No H-bonds generated for 'chain 'F' and resid 433 through 435' Processing helix chain 'F' and resid 437 through 445 removed outlier: 3.759A pdb=" N ALA F 441 " --> pdb=" O ARG F 437 " (cutoff:3.500A) removed outlier: 4.041A 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 539 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.607A pdb=" N THR F 564 " --> pdb=" O ASN F 560 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 4.269A 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 156 through 164 removed outlier: 6.467A pdb=" N VAL A 124 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 122 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG A 97 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 124 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 99 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N HIS A 126 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 3 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N CYS A 100 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 5 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 4 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 33 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS A 6 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N THR A 35 " --> pdb=" O CYS A 6 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 30 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 62 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 32 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 64 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A 34 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 192 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 262 removed outlier: 7.578A pdb=" N LYS A 256 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.299A 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: 5.913A pdb=" N ILE A 349 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N HIS A 260 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N CYS A 351 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N HIS A 262 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N VAL A 389 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N GLY A 428 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 391 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP A 430 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 393 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 432 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.831A pdb=" N GLY B 162 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU B 123 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 97 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE B 125 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 3 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N CYS B 100 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 5 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B 35 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 30 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER B 62 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 32 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 64 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR B 34 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 188 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 262 removed outlier: 7.464A pdb=" N LYS B 256 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA B 347 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU B 258 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE B 349 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N HIS B 260 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N CYS B 351 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N HIS B 262 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 345 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN B 390 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA B 347 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 392 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 349 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR B 394 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 351 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR B 396 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 426 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 391 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 428 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 427 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR B 459 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 429 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N HIS B 461 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 431 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.677A 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: 7.324A pdb=" N LYS C 256 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA C 347 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU C 258 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 349 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N HIS C 260 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N CYS C 351 " --> pdb=" O HIS C 260 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N HIS C 262 " --> pdb=" O CYS C 351 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL C 389 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N GLY C 428 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 391 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP C 430 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 393 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.862A 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: 7.388A pdb=" N LYS D 256 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA D 347 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 258 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 349 " --> pdb=" O GLU D 258 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N HIS D 260 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N CYS D 351 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N HIS D 262 " --> pdb=" O CYS D 351 " (cutoff:3.500A) removed outlier: 11.354A pdb=" N VAL D 389 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N GLY D 428 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 391 " --> pdb=" O GLY D 428 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP D 430 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 393 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.844A 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: 7.404A pdb=" N LYS E 256 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA E 347 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU E 258 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE E 349 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N HIS E 260 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N CYS E 351 " --> pdb=" O HIS E 260 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N HIS E 262 " --> pdb=" O CYS E 351 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA E 345 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN E 390 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.238A 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: 6.344A pdb=" N ILE E 349 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR E 394 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS E 351 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 11.268A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.794A 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: 7.609A pdb=" N LYS F 256 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 347 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU F 258 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE F 349 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N HIS F 260 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N CYS F 351 " --> pdb=" O HIS F 260 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N HIS F 262 " --> pdb=" O CYS F 351 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA F 345 " --> pdb=" O HIS F 388 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN F 390 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA F 347 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU F 392 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE F 349 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR F 394 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS F 351 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL F 426 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 391 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY F 428 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3593 1.31 - 1.44: 5859 1.44 - 1.56: 12657 1.56 - 1.69: 41 1.69 - 1.81: 112 Bond restraints: 22262 Sorted by residual: bond pdb=" CA SER F 556 " pdb=" CB SER F 556 " ideal model delta sigma weight residual 1.534 1.465 0.070 1.60e-02 3.91e+03 1.90e+01 bond pdb=" CA SER F 553 " pdb=" CB SER F 553 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.63e-02 3.76e+03 1.43e+01 bond pdb=" C PRO C 296 " pdb=" O PRO C 296 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.16e-02 7.43e+03 1.39e+01 bond pdb=" CA SER C 553 " pdb=" CB SER C 553 " ideal model delta sigma weight residual 1.536 1.482 0.054 1.58e-02 4.01e+03 1.18e+01 bond pdb=" N PRO F 301 " pdb=" CA PRO F 301 " ideal model delta sigma weight residual 1.465 1.428 0.038 1.19e-02 7.06e+03 1.00e+01 ... (remaining 22257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 30074 2.66 - 5.33: 325 5.33 - 7.99: 23 7.99 - 10.66: 0 10.66 - 13.32: 2 Bond angle restraints: 30424 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 126.55 13.32 1.00e+00 1.00e+00 1.77e+02 angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 128.94 10.93 1.00e+00 1.00e+00 1.19e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 129.92 6.91 1.00e+00 1.00e+00 4.77e+01 angle pdb=" C PRO E 296 " pdb=" CA PRO E 296 " pdb=" CB PRO E 296 " ideal model delta sigma weight residual 111.56 104.52 7.04 1.09e+00 8.42e-01 4.17e+01 angle pdb=" N ILE A 219 " pdb=" CA ILE A 219 " pdb=" C ILE A 219 " ideal model delta sigma weight residual 113.42 106.26 7.16 1.17e+00 7.31e-01 3.75e+01 ... (remaining 30419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12123 17.97 - 35.95: 962 35.95 - 53.92: 290 53.92 - 71.90: 79 71.90 - 89.87: 26 Dihedral angle restraints: 13480 sinusoidal: 5557 harmonic: 7923 Sorted by residual: dihedral pdb=" CA TRP E 298 " pdb=" C TRP E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta harmonic sigma weight residual 0.00 29.02 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA TRP B 298 " pdb=" C TRP B 298 " pdb=" N PRO B 299 " pdb=" CA PRO B 299 " ideal model delta harmonic sigma weight residual 0.00 28.36 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLU A 217 " pdb=" C GLU A 217 " pdb=" N GLY A 218 " pdb=" CA GLY A 218 " ideal model delta harmonic sigma weight residual -180.00 -151.92 -28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 13477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2848 0.056 - 0.112: 457 0.112 - 0.168: 60 0.168 - 0.223: 10 0.223 - 0.279: 6 Chirality restraints: 3381 Sorted by residual: 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 -2.91 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C4' ATP C 701 " pdb=" C3' ATP C 701 " pdb=" C5' ATP C 701 " pdb=" O4' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C2' ATP D 701 " pdb=" C1' ATP D 701 " pdb=" C3' ATP D 701 " pdb=" O2' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.94 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3378 not shown) Planarity restraints: 3955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 214 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C ALA B 214 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA B 214 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 215 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 175 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO B 176 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 519 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO E 520 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 520 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 520 " 0.035 5.00e-02 4.00e+02 ... (remaining 3952 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 204 2.57 - 3.15: 17710 3.15 - 3.74: 34909 3.74 - 4.32: 49316 4.32 - 4.90: 82533 Nonbonded interactions: 184672 Sorted by model distance: nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 703 " model vdw 1.990 2.230 nonbonded pdb=" OD1 ASP A 548 " pdb="ZN ZN A 703 " model vdw 2.014 2.230 nonbonded pdb=" OD1 ASP F 548 " pdb="ZN ZN F 703 " model vdw 2.014 2.230 nonbonded pdb=" OD1 ASP D 548 " pdb="ZN ZN D 703 " model vdw 2.025 2.230 nonbonded pdb=" OD1 ASP E 548 " pdb="ZN ZN E 703 " model vdw 2.050 2.230 ... (remaining 184667 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 397 or resid 404 through 433 or resid 447 throug \ h 703)) selection = chain 'B' } 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: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.500 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.315 22280 Z= 0.264 Angle : 0.632 13.322 30424 Z= 0.378 Chirality : 0.045 0.279 3381 Planarity : 0.006 0.100 3955 Dihedral : 15.315 89.874 8340 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.15 % Favored : 95.38 % Rotamer: Outliers : 2.24 % Allowed : 11.13 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 0.33 (0.16), residues: 2726 helix: 1.03 (0.14), residues: 1289 sheet: -0.53 (0.29), residues: 336 loop : -0.38 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 403 TYR 0.014 0.001 TYR B 105 PHE 0.017 0.001 PHE B 67 TRP 0.025 0.002 TRP C 298 HIS 0.008 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.24 (22262) covalent geometry : angle 0.63179 / 0.38 (30424) hydrogen bonds : bond 0.17786 / 12.05 ( 987) hydrogen bonds : angle 6.20887 / 4.44 ( 2778) metal coordination : bond 0.10369 / 6.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 615 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.8274 (mtp) cc_final: 0.7913 (mtp) REVERT: A 29 GLU cc_start: 0.6694 (tt0) cc_final: 0.4205 (mt-10) REVERT: A 40 ILE cc_start: 0.8920 (mm) cc_final: 0.8702 (mm) REVERT: A 60 SER cc_start: 0.8284 (t) cc_final: 0.7886 (p) REVERT: A 112 MET cc_start: 0.8274 (mmm) cc_final: 0.8001 (mmt) REVERT: A 160 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: A 177 SER cc_start: 0.8639 (m) cc_final: 0.8243 (t) REVERT: A 182 SER cc_start: 0.8297 (t) cc_final: 0.8055 (m) REVERT: A 184 LEU cc_start: 0.8383 (mt) cc_final: 0.8131 (mt) REVERT: A 195 ASP cc_start: 0.7164 (p0) cc_final: 0.6772 (p0) REVERT: A 211 HIS cc_start: 0.8026 (m170) cc_final: 0.7379 (m170) REVERT: A 217 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6069 (pp20) REVERT: A 376 GLN cc_start: 0.8488 (tt0) cc_final: 0.8167 (tt0) REVERT: A 492 SER cc_start: 0.8766 (t) cc_final: 0.8328 (p) REVERT: B 29 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7264 (mp0) REVERT: B 51 PHE cc_start: 0.8739 (m-10) cc_final: 0.8393 (m-10) REVERT: B 88 LEU cc_start: 0.8415 (mt) cc_final: 0.8179 (mp) REVERT: B 112 MET cc_start: 0.8522 (mmm) cc_final: 0.8249 (mmm) REVERT: B 164 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7242 (mp0) REVERT: B 169 GLN cc_start: 0.7780 (mp10) cc_final: 0.7430 (mp10) REVERT: B 174 SER cc_start: 0.8040 (p) cc_final: 0.7796 (m) REVERT: B 182 SER cc_start: 0.8189 (t) cc_final: 0.7987 (m) REVERT: B 184 LEU cc_start: 0.7940 (mp) cc_final: 0.7642 (mt) REVERT: B 271 GLU cc_start: 0.7728 (tp30) cc_final: 0.7452 (tp30) REVERT: B 350 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8495 (mtt90) REVERT: B 472 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: B 517 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8755 (mmmt) REVERT: C 308 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7876 (tp30) REVERT: C 405 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7503 (mmm-85) REVERT: C 430 ASP cc_start: 0.8159 (t0) cc_final: 0.7844 (t0) REVERT: C 461 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7906 (m-70) REVERT: D 436 ASP cc_start: 0.7971 (t70) cc_final: 0.7751 (t0) REVERT: E 308 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7356 (mm-30) REVERT: E 378 MET cc_start: 0.8711 (mtp) cc_final: 0.8268 (mtp) REVERT: E 430 ASP cc_start: 0.8112 (t70) cc_final: 0.7772 (t0) REVERT: E 461 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8215 (m90) REVERT: E 507 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7067 (mt-10) REVERT: F 247 ASP cc_start: 0.7620 (m-30) cc_final: 0.7333 (m-30) REVERT: F 279 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7887 (mm-30) REVERT: F 497 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: F 507 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8078 (mt-10) outliers start: 50 outliers final: 9 residues processed: 643 average time/residue: 0.8547 time to fit residues: 608.5546 Evaluate side-chains 546 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 532 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 CYS Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain E residue 278 GLN 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 F residue 439 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 96 HIS ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 211 HIS A 282 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 211 HIS B 546 ASN B 560 ASN C 246 GLN ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 473 GLN C 513 ASN C 554 GLN C 585 GLN D 246 GLN D 278 GLN D 316 ASN D 409 HIS D 585 GLN D 591 GLN E 234 HIS E 252 GLN E 269 HIS E 390 ASN E 422 ASN E 554 GLN E 585 GLN F 355 ASN F 390 ASN F 422 ASN F 513 ASN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 GLN F 585 GLN F 603 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095835 restraints weight = 33951.124| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.99 r_work: 0.3112 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22280 Z= 0.155 Angle : 0.616 7.331 30424 Z= 0.313 Chirality : 0.042 0.151 3381 Planarity : 0.006 0.085 3955 Dihedral : 9.097 83.056 3299 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.26 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 16.11 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 0.76 (0.17), residues: 2726 helix: 1.45 (0.15), residues: 1308 sheet: -0.56 (0.28), residues: 327 loop : -0.21 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 85 TYR 0.009 0.001 TYR F 336 PHE 0.016 0.001 PHE B 59 TRP 0.018 0.001 TRP A 86 HIS 0.012 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (22262) covalent geometry : angle 0.61635 / 0.31 (30424) hydrogen bonds : bond 0.04622 / 3.05 ( 987) hydrogen bonds : angle 4.89569 / 3.51 ( 2778) metal coordination : bond 0.00747 / 0.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 543 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7577 (tt0) cc_final: 0.7295 (mt-10) REVERT: A 53 MET cc_start: 0.8191 (ptt) cc_final: 0.7960 (ttp) REVERT: A 196 MET cc_start: 0.8411 (tpp) cc_final: 0.8019 (tpt) REVERT: A 207 GLU cc_start: 0.7730 (pp20) cc_final: 0.7337 (pp20) REVERT: A 217 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: A 376 GLN cc_start: 0.8691 (tt0) cc_final: 0.8422 (tt0) REVERT: A 385 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8215 (ttp-110) REVERT: A 403 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7455 (mmm-85) REVERT: A 492 SER cc_start: 0.8527 (t) cc_final: 0.8257 (m) REVERT: A 525 GLN cc_start: 0.8298 (mp10) cc_final: 0.8019 (mp10) REVERT: B 29 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8144 (mp0) REVERT: B 88 LEU cc_start: 0.8852 (mt) cc_final: 0.8641 (mp) REVERT: B 112 MET cc_start: 0.8549 (mmm) cc_final: 0.8323 (mmm) REVERT: B 130 GLU cc_start: 0.8381 (tt0) cc_final: 0.7966 (tt0) REVERT: B 169 GLN cc_start: 0.8115 (mp10) cc_final: 0.7890 (mp10) REVERT: B 171 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8335 (mtm-85) REVERT: B 182 SER cc_start: 0.8333 (t) cc_final: 0.8109 (m) REVERT: B 192 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7783 (ptm160) REVERT: B 271 GLU cc_start: 0.7464 (tp30) cc_final: 0.6969 (tp30) REVERT: B 275 LYS cc_start: 0.8473 (ttmm) cc_final: 0.7890 (ttmm) REVERT: B 329 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8475 (ttp80) REVERT: B 350 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8406 (mtt90) REVERT: B 517 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8736 (mmmt) REVERT: B 591 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8135 (mp10) REVERT: C 308 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7744 (tp30) REVERT: C 383 GLU cc_start: 0.7750 (tp30) cc_final: 0.7429 (tp30) REVERT: C 405 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7600 (mtm-85) REVERT: C 461 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.7873 (m-70) REVERT: C 469 GLU cc_start: 0.8282 (tp30) cc_final: 0.7899 (mm-30) REVERT: C 526 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7410 (tm-30) REVERT: D 333 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.8058 (mmt90) REVERT: D 436 ASP cc_start: 0.7726 (t70) cc_final: 0.7486 (t0) REVERT: D 501 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: E 243 ASP cc_start: 0.7734 (t0) cc_final: 0.7485 (t0) REVERT: E 300 ILE cc_start: 0.8617 (mp) cc_final: 0.8381 (mp) REVERT: E 308 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6969 (mm-30) REVERT: E 309 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7604 (mtp180) REVERT: E 378 MET cc_start: 0.8637 (mtp) cc_final: 0.8222 (mtp) REVERT: E 383 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 403 ARG cc_start: 0.6460 (mmp80) cc_final: 0.5951 (mmp80) REVERT: E 507 GLU cc_start: 0.8775 (mt-10) cc_final: 0.6910 (pt0) REVERT: E 603 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: F 247 ASP cc_start: 0.8126 (m-30) cc_final: 0.7770 (m-30) REVERT: F 279 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 313 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8530 (mp) REVERT: F 315 ASP cc_start: 0.7719 (t0) cc_final: 0.7382 (t0) REVERT: F 469 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7727 (mm-30) REVERT: F 507 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8163 (mt-10) REVERT: F 575 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7450 (mm-30) outliers start: 61 outliers final: 25 residues processed: 571 average time/residue: 0.8502 time to fit residues: 536.7002 Evaluate side-chains 553 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 522 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 143 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 228 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 282 ASN B 282 ASN ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN D 278 GLN D 316 ASN D 409 HIS D 585 GLN E 252 GLN E 269 HIS E 355 ASN E 554 GLN E 585 GLN F 355 ASN F 473 GLN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096080 restraints weight = 34111.213| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3110 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22280 Z= 0.131 Angle : 0.563 6.828 30424 Z= 0.285 Chirality : 0.040 0.134 3381 Planarity : 0.006 0.074 3955 Dihedral : 8.777 83.532 3292 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.23 % Favored : 96.48 % Rotamer: Outliers : 3.10 % Allowed : 17.37 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.00 (0.17), residues: 2726 helix: 1.68 (0.15), residues: 1313 sheet: -0.51 (0.28), residues: 341 loop : -0.12 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 385 TYR 0.008 0.001 TYR B 50 PHE 0.019 0.001 PHE A 59 TRP 0.015 0.001 TRP A 364 HIS 0.009 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (22262) covalent geometry : angle 0.56284 / 0.28 (30424) hydrogen bonds : bond 0.04021 / 2.66 ( 987) hydrogen bonds : angle 4.62404 / 3.34 ( 2778) metal coordination : bond 0.00249 / 0.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 524 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7708 (tt0) cc_final: 0.7118 (mt-10) REVERT: A 53 MET cc_start: 0.8190 (ptt) cc_final: 0.7919 (ttp) REVERT: A 58 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6201 (ttt180) REVERT: A 144 LEU cc_start: 0.8225 (mp) cc_final: 0.7084 (mp) REVERT: A 217 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: A 279 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: A 376 GLN cc_start: 0.8771 (tt0) cc_final: 0.8475 (tt0) REVERT: A 385 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8094 (ttp-110) REVERT: A 403 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7360 (mmm-85) REVERT: A 492 SER cc_start: 0.8479 (t) cc_final: 0.8207 (m) REVERT: A 525 GLN cc_start: 0.8343 (mp10) cc_final: 0.8004 (mp10) REVERT: B 88 LEU cc_start: 0.8865 (mt) cc_final: 0.8645 (mp) REVERT: B 160 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: B 164 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 171 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8204 (mtm-85) REVERT: B 282 ASN cc_start: 0.8609 (m-40) cc_final: 0.8389 (m-40) REVERT: B 350 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8450 (mtt90) REVERT: B 517 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8737 (mmmt) REVERT: C 308 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7664 (tp30) REVERT: C 312 ARG cc_start: 0.8264 (mmp80) cc_final: 0.8026 (mmp80) REVERT: C 376 GLN cc_start: 0.8069 (tt0) cc_final: 0.7860 (tt0) REVERT: C 405 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7613 (mtm-85) REVERT: C 430 ASP cc_start: 0.8320 (t0) cc_final: 0.7884 (t0) REVERT: C 461 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7923 (m-70) REVERT: C 469 GLU cc_start: 0.8412 (tp30) cc_final: 0.8083 (mm-30) REVERT: C 526 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 333 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.8101 (mmt90) REVERT: D 436 ASP cc_start: 0.7735 (t70) cc_final: 0.7452 (t0) REVERT: D 501 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: D 591 GLN cc_start: 0.8011 (tp40) cc_final: 0.7571 (tp40) REVERT: E 300 ILE cc_start: 0.8539 (mp) cc_final: 0.8305 (mm) REVERT: E 308 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6989 (mm-30) REVERT: E 309 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7622 (mtp180) REVERT: E 378 MET cc_start: 0.8633 (mtp) cc_final: 0.8231 (mtp) REVERT: E 383 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 403 ARG cc_start: 0.6441 (mmp80) cc_final: 0.5995 (mmp80) REVERT: E 497 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8034 (ttp-110) REVERT: E 507 GLU cc_start: 0.8779 (mt-10) cc_final: 0.7219 (pm20) REVERT: E 603 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: F 247 ASP cc_start: 0.8109 (m-30) cc_final: 0.7757 (m-30) REVERT: F 279 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7945 (mm-30) REVERT: F 313 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8497 (mp) REVERT: F 315 ASP cc_start: 0.7834 (t0) cc_final: 0.7534 (t0) REVERT: F 507 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8193 (mt-10) REVERT: F 575 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7430 (mm-30) outliers start: 69 outliers final: 31 residues processed: 550 average time/residue: 0.8733 time to fit residues: 529.3032 Evaluate side-chains 549 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 510 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 221 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 282 ASN A 591 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 HIS C 375 GLN C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 234 HIS E 252 GLN E 355 ASN E 554 GLN E 580 GLN E 585 GLN F 355 ASN F 603 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095105 restraints weight = 34125.483| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22280 Z= 0.150 Angle : 0.567 7.515 30424 Z= 0.288 Chirality : 0.041 0.150 3381 Planarity : 0.006 0.066 3955 Dihedral : 8.563 83.939 3290 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.60 % Favored : 96.07 % Rotamer: Outliers : 3.59 % Allowed : 18.36 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.09 (0.17), residues: 2726 helix: 1.76 (0.15), residues: 1312 sheet: -0.51 (0.28), residues: 343 loop : -0.04 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 49 TYR 0.011 0.001 TYR B 50 PHE 0.030 0.001 PHE B 59 TRP 0.017 0.001 TRP B 167 HIS 0.009 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (22262) covalent geometry : angle 0.56713 / 0.29 (30424) hydrogen bonds : bond 0.03937 / 2.60 ( 987) hydrogen bonds : angle 4.50655 / 3.26 ( 2778) metal coordination : bond 0.00344 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 530 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7764 (tt0) cc_final: 0.7267 (mt-10) REVERT: A 49 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7805 (ttp-170) REVERT: A 58 ARG cc_start: 0.6799 (ttt180) cc_final: 0.6305 (ttt180) REVERT: A 170 LEU cc_start: 0.8871 (mt) cc_final: 0.8645 (mt) REVERT: A 217 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: A 279 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: A 376 GLN cc_start: 0.8732 (tt0) cc_final: 0.8465 (tt0) REVERT: A 403 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7320 (mmm-85) REVERT: A 473 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8409 (mm-40) REVERT: A 492 SER cc_start: 0.8476 (t) cc_final: 0.8221 (m) REVERT: B 77 MET cc_start: 0.8159 (mtm) cc_final: 0.7949 (mtm) REVERT: B 88 LEU cc_start: 0.8904 (mt) cc_final: 0.8699 (mp) REVERT: B 160 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7870 (mtt-85) REVERT: B 164 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 171 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8196 (mtm-85) REVERT: B 271 GLU cc_start: 0.7573 (tp30) cc_final: 0.7017 (tp30) REVERT: B 315 ASP cc_start: 0.8530 (m-30) cc_final: 0.8263 (m-30) REVERT: B 350 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8486 (mtt90) REVERT: B 517 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8728 (mmmt) REVERT: C 308 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7721 (tp30) REVERT: C 405 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7606 (mtm-85) REVERT: C 430 ASP cc_start: 0.8313 (t0) cc_final: 0.7912 (t0) REVERT: C 461 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.7935 (m-70) REVERT: C 469 GLU cc_start: 0.8426 (tp30) cc_final: 0.8083 (mm-30) REVERT: C 526 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 333 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8083 (mmt90) REVERT: D 436 ASP cc_start: 0.7795 (t70) cc_final: 0.7536 (t0) REVERT: D 501 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: D 591 GLN cc_start: 0.8048 (tp40) cc_final: 0.7687 (tt0) REVERT: E 300 ILE cc_start: 0.8538 (mp) cc_final: 0.8296 (mp) REVERT: E 303 GLU cc_start: 0.7564 (pp20) cc_final: 0.7222 (pp20) REVERT: E 308 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7004 (mm-30) REVERT: E 378 MET cc_start: 0.8613 (mtp) cc_final: 0.8189 (mtp) REVERT: E 383 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 403 ARG cc_start: 0.6475 (mmp80) cc_final: 0.6088 (mmp80) REVERT: E 497 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8108 (ttm-80) REVERT: E 507 GLU cc_start: 0.8784 (mt-10) cc_final: 0.7181 (pm20) REVERT: E 603 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: F 247 ASP cc_start: 0.8138 (m-30) cc_final: 0.7794 (m-30) REVERT: F 258 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: F 279 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7951 (mm-30) REVERT: F 313 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8608 (mp) REVERT: F 315 ASP cc_start: 0.7947 (t0) cc_final: 0.7696 (t0) REVERT: F 383 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7647 (tm-30) REVERT: F 492 SER cc_start: 0.8649 (t) cc_final: 0.8400 (m) REVERT: F 507 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8213 (mt-10) REVERT: F 549 ASN cc_start: 0.8934 (m110) cc_final: 0.8682 (m110) REVERT: F 575 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7437 (mm-30) outliers start: 80 outliers final: 36 residues processed: 561 average time/residue: 0.8214 time to fit residues: 509.0278 Evaluate side-chains 567 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 522 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 459 THR Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.0010 chunk 190 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 193 optimal weight: 0.0770 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 282 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 252 GLN E 355 ASN E 554 GLN E 580 GLN E 585 GLN F 355 ASN F 422 ASN F 485 HIS F 603 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094622 restraints weight = 34008.409| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.97 r_work: 0.3094 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22280 Z= 0.189 Angle : 0.583 7.847 30424 Z= 0.295 Chirality : 0.042 0.141 3381 Planarity : 0.006 0.065 3955 Dihedral : 8.412 84.220 3288 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.60 % Favored : 96.11 % Rotamer: Outliers : 3.68 % Allowed : 18.76 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.14 (0.17), residues: 2726 helix: 1.78 (0.15), residues: 1304 sheet: -0.52 (0.28), residues: 348 loop : 0.04 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 385 TYR 0.011 0.001 TYR B 50 PHE 0.035 0.002 PHE B 59 TRP 0.020 0.002 TRP E 237 HIS 0.010 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (22262) covalent geometry : angle 0.58311 / 0.30 (30424) hydrogen bonds : bond 0.04163 / 2.75 ( 987) hydrogen bonds : angle 4.49025 / 3.24 ( 2778) metal coordination : bond 0.00359 / 0.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 531 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7824 (tt0) cc_final: 0.7415 (mt-10) REVERT: A 49 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7794 (ttp-170) REVERT: A 93 GLN cc_start: 0.8237 (mt0) cc_final: 0.8012 (mp10) REVERT: A 130 GLU cc_start: 0.7996 (mp0) cc_final: 0.7765 (mp0) REVERT: A 189 HIS cc_start: 0.7852 (m170) cc_final: 0.7651 (m170) REVERT: A 196 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8510 (mtm) REVERT: A 217 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: A 376 GLN cc_start: 0.8752 (tt0) cc_final: 0.8445 (tt0) REVERT: A 403 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: A 492 SER cc_start: 0.8513 (t) cc_final: 0.8255 (m) REVERT: B 171 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8026 (mtm-85) REVERT: B 271 GLU cc_start: 0.7749 (tp30) cc_final: 0.7338 (tp30) REVERT: B 279 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: B 282 ASN cc_start: 0.8652 (m-40) cc_final: 0.8424 (m-40) REVERT: B 315 ASP cc_start: 0.8553 (m-30) cc_final: 0.8284 (m-30) REVERT: B 350 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8355 (mtt90) REVERT: B 517 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8739 (mmmt) REVERT: B 524 GLU cc_start: 0.7227 (pp20) cc_final: 0.7006 (pp20) REVERT: C 308 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7735 (tp30) REVERT: C 383 GLU cc_start: 0.7745 (tp30) cc_final: 0.7501 (tp30) REVERT: C 405 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7613 (mtm-85) REVERT: C 430 ASP cc_start: 0.8340 (t0) cc_final: 0.7938 (t0) REVERT: C 461 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7994 (m-70) REVERT: C 469 GLU cc_start: 0.8410 (tp30) cc_final: 0.8088 (mm-30) REVERT: C 525 GLN cc_start: 0.8412 (tp40) cc_final: 0.8160 (tp40) REVERT: C 526 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 333 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8079 (mmt90) REVERT: D 436 ASP cc_start: 0.7804 (t70) cc_final: 0.7530 (t0) REVERT: D 501 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 591 GLN cc_start: 0.8121 (tp40) cc_final: 0.7738 (tt0) REVERT: E 300 ILE cc_start: 0.8581 (mp) cc_final: 0.8343 (mp) REVERT: E 303 GLU cc_start: 0.7636 (pp20) cc_final: 0.7263 (pp20) REVERT: E 308 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7030 (mm-30) REVERT: E 378 MET cc_start: 0.8607 (mtp) cc_final: 0.8178 (mtp) REVERT: E 403 ARG cc_start: 0.6493 (mmp80) cc_final: 0.6213 (mmp80) REVERT: E 497 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8125 (ttm-80) REVERT: E 507 GLU cc_start: 0.8768 (mt-10) cc_final: 0.7190 (pt0) REVERT: E 603 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: F 247 ASP cc_start: 0.8164 (m-30) cc_final: 0.7816 (m-30) REVERT: F 279 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7938 (mm-30) REVERT: F 313 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8676 (mp) REVERT: F 315 ASP cc_start: 0.8084 (t70) cc_final: 0.7869 (t0) REVERT: F 383 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7741 (tm-30) REVERT: F 492 SER cc_start: 0.8723 (t) cc_final: 0.8465 (m) REVERT: F 507 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 575 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7475 (mm-30) outliers start: 82 outliers final: 41 residues processed: 562 average time/residue: 0.8443 time to fit residues: 524.6265 Evaluate side-chains 568 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 519 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 222 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 264 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 282 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 GLN F 355 ASN F 580 GLN F 603 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094814 restraints weight = 34033.500| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.97 r_work: 0.3107 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22280 Z= 0.157 Angle : 0.580 8.619 30424 Z= 0.293 Chirality : 0.041 0.135 3381 Planarity : 0.006 0.063 3955 Dihedral : 8.321 86.145 3288 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.63 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 20.24 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.23 (0.17), residues: 2726 helix: 1.85 (0.15), residues: 1306 sheet: -0.43 (0.29), residues: 337 loop : 0.06 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 385 TYR 0.009 0.001 TYR F 336 PHE 0.033 0.001 PHE B 59 TRP 0.024 0.001 TRP E 237 HIS 0.011 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (22262) covalent geometry : angle 0.57969 / 0.29 (30424) hydrogen bonds : bond 0.03917 / 2.58 ( 987) hydrogen bonds : angle 4.41596 / 3.19 ( 2778) metal coordination : bond 0.00318 / 0.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 531 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7833 (tt0) cc_final: 0.7521 (mt-10) REVERT: A 49 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7742 (ttp-170) REVERT: A 53 MET cc_start: 0.8117 (ptt) cc_final: 0.7869 (ttp) REVERT: A 71 ARG cc_start: 0.7663 (mtt-85) cc_final: 0.7364 (mtm-85) REVERT: A 130 GLU cc_start: 0.7993 (mp0) cc_final: 0.7752 (mp0) REVERT: A 144 LEU cc_start: 0.8140 (mp) cc_final: 0.7756 (mp) REVERT: A 189 HIS cc_start: 0.7855 (m170) cc_final: 0.7651 (m170) REVERT: A 196 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: A 198 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 199 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7909 (mtp85) REVERT: A 217 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: A 376 GLN cc_start: 0.8755 (tt0) cc_final: 0.8302 (tt0) REVERT: A 380 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8476 (mt-10) REVERT: A 403 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.7296 (mmm-85) REVERT: A 492 SER cc_start: 0.8508 (t) cc_final: 0.8243 (m) REVERT: A 495 LEU cc_start: 0.8554 (tp) cc_final: 0.8335 (tp) REVERT: B 25 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7858 (mm-40) REVERT: B 171 ARG cc_start: 0.8405 (ttp-110) cc_final: 0.8008 (mtm-85) REVERT: B 271 GLU cc_start: 0.7767 (tp30) cc_final: 0.7400 (tp30) REVERT: B 279 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: B 302 GLU cc_start: 0.7825 (pm20) cc_final: 0.7558 (pm20) REVERT: B 315 ASP cc_start: 0.8546 (m-30) cc_final: 0.8288 (m-30) REVERT: B 350 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8357 (mtt90) REVERT: B 517 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8738 (mmmt) REVERT: B 524 GLU cc_start: 0.7249 (pp20) cc_final: 0.6952 (pp20) REVERT: C 308 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7734 (tp30) REVERT: C 430 ASP cc_start: 0.8335 (t0) cc_final: 0.7945 (t0) REVERT: C 461 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7975 (m-70) REVERT: C 469 GLU cc_start: 0.8392 (tp30) cc_final: 0.8071 (mm-30) REVERT: C 526 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 333 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8094 (mmt90) REVERT: D 436 ASP cc_start: 0.7751 (t70) cc_final: 0.7497 (t0) REVERT: D 501 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: D 591 GLN cc_start: 0.8108 (tp40) cc_final: 0.7727 (tt0) REVERT: E 300 ILE cc_start: 0.8565 (mp) cc_final: 0.8316 (mp) REVERT: E 303 GLU cc_start: 0.7691 (pp20) cc_final: 0.7365 (pp20) REVERT: E 308 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7018 (mm-30) REVERT: E 378 MET cc_start: 0.8584 (mtp) cc_final: 0.8148 (mtp) REVERT: E 383 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 403 ARG cc_start: 0.6412 (mmp80) cc_final: 0.6211 (mmp80) REVERT: E 497 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8121 (ttm-80) REVERT: E 507 GLU cc_start: 0.8757 (mt-10) cc_final: 0.7531 (mp0) REVERT: E 603 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: F 247 ASP cc_start: 0.8183 (m-30) cc_final: 0.7845 (m-30) REVERT: F 279 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7920 (mm-30) REVERT: F 313 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8686 (mp) REVERT: F 383 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7769 (tm-30) REVERT: F 492 SER cc_start: 0.8710 (t) cc_final: 0.8454 (m) REVERT: F 507 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 575 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7432 (mm-30) outliers start: 66 outliers final: 40 residues processed: 553 average time/residue: 0.8167 time to fit residues: 498.4316 Evaluate side-chains 573 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 524 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 228 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 143 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 282 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 485 HIS C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 234 HIS E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 GLN F 603 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094279 restraints weight = 34166.016| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.99 r_work: 0.3091 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22280 Z= 0.172 Angle : 0.589 9.214 30424 Z= 0.297 Chirality : 0.042 0.139 3381 Planarity : 0.006 0.083 3955 Dihedral : 8.251 86.061 3288 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.63 % Favored : 96.04 % Rotamer: Outliers : 3.46 % Allowed : 20.24 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.24 (0.17), residues: 2726 helix: 1.86 (0.15), residues: 1303 sheet: -0.35 (0.29), residues: 335 loop : 0.03 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 385 TYR 0.009 0.001 TYR C 336 PHE 0.038 0.002 PHE B 59 TRP 0.032 0.001 TRP E 237 HIS 0.011 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (22262) covalent geometry : angle 0.58900 / 0.30 (30424) hydrogen bonds : bond 0.03970 / 2.62 ( 987) hydrogen bonds : angle 4.41656 / 3.19 ( 2778) metal coordination : bond 0.00347 / 0.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 526 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7839 (tt0) cc_final: 0.7499 (mt-10) REVERT: A 71 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7228 (mtm-85) REVERT: A 130 GLU cc_start: 0.8020 (mp0) cc_final: 0.7774 (mp0) REVERT: A 196 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8663 (mtm) REVERT: A 198 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 217 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: A 376 GLN cc_start: 0.8768 (tt0) cc_final: 0.8393 (tt0) REVERT: A 379 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 403 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7306 (mmm-85) REVERT: A 492 SER cc_start: 0.8514 (t) cc_final: 0.8260 (m) REVERT: B 25 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7849 (mm-40) REVERT: B 171 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.7966 (mtm-85) REVERT: B 271 GLU cc_start: 0.7878 (tp30) cc_final: 0.7524 (tp30) REVERT: B 279 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: B 282 ASN cc_start: 0.8659 (m-40) cc_final: 0.8455 (m-40) REVERT: B 302 GLU cc_start: 0.7787 (pm20) cc_final: 0.7499 (mp0) REVERT: B 315 ASP cc_start: 0.8551 (m-30) cc_final: 0.8287 (m-30) REVERT: B 517 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8748 (mmmt) REVERT: B 524 GLU cc_start: 0.7315 (pp20) cc_final: 0.7087 (pp20) REVERT: C 308 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7683 (tp30) REVERT: C 312 ARG cc_start: 0.8335 (mmp80) cc_final: 0.8119 (mmp80) REVERT: C 430 ASP cc_start: 0.8344 (t0) cc_final: 0.7972 (t0) REVERT: C 461 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: C 469 GLU cc_start: 0.8412 (tp30) cc_final: 0.8085 (mm-30) REVERT: C 525 GLN cc_start: 0.8375 (tp40) cc_final: 0.8137 (tp40) REVERT: C 526 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7321 (tm-30) REVERT: D 333 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8124 (mmt90) REVERT: D 436 ASP cc_start: 0.7739 (t70) cc_final: 0.7517 (t0) REVERT: D 591 GLN cc_start: 0.8135 (tp40) cc_final: 0.7744 (tt0) REVERT: E 300 ILE cc_start: 0.8607 (mp) cc_final: 0.8365 (mp) REVERT: E 303 GLU cc_start: 0.7710 (pp20) cc_final: 0.7380 (pp20) REVERT: E 308 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7057 (mm-30) REVERT: E 329 ARG cc_start: 0.7828 (tmm-80) cc_final: 0.7474 (ttt90) REVERT: E 378 MET cc_start: 0.8610 (mtp) cc_final: 0.8190 (mtp) REVERT: E 383 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7907 (tm-30) REVERT: E 403 ARG cc_start: 0.6338 (mmp80) cc_final: 0.6023 (mmp80) REVERT: E 497 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8095 (ttm-80) REVERT: E 507 GLU cc_start: 0.8767 (mt-10) cc_final: 0.7542 (mp0) REVERT: E 603 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: F 247 ASP cc_start: 0.8179 (m-30) cc_final: 0.7839 (m-30) REVERT: F 279 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 313 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mp) REVERT: F 383 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7776 (tm-30) REVERT: F 492 SER cc_start: 0.8721 (t) cc_final: 0.8467 (m) REVERT: F 507 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8188 (mt-10) REVERT: F 575 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7457 (mm-30) outliers start: 77 outliers final: 45 residues processed: 558 average time/residue: 0.8611 time to fit residues: 531.1863 Evaluate side-chains 568 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 515 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 185 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 269 HIS A 282 ASN C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 GLN F 603 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095317 restraints weight = 34245.026| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.99 r_work: 0.3104 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22280 Z= 0.151 Angle : 0.594 9.622 30424 Z= 0.301 Chirality : 0.041 0.143 3381 Planarity : 0.005 0.074 3955 Dihedral : 8.063 87.816 3284 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.60 % Favored : 96.07 % Rotamer: Outliers : 3.10 % Allowed : 21.05 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.29 (0.17), residues: 2726 helix: 1.88 (0.15), residues: 1313 sheet: -0.29 (0.28), residues: 343 loop : 0.06 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 385 TYR 0.009 0.001 TYR F 336 PHE 0.035 0.001 PHE B 59 TRP 0.036 0.001 TRP E 237 HIS 0.012 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (22262) covalent geometry : angle 0.59355 / 0.30 (30424) hydrogen bonds : bond 0.03809 / 2.51 ( 987) hydrogen bonds : angle 4.36853 / 3.16 ( 2778) metal coordination : bond 0.00297 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 520 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7820 (tt0) cc_final: 0.7517 (mt-10) REVERT: A 71 ARG cc_start: 0.7680 (mtt-85) cc_final: 0.7328 (mtm-85) REVERT: A 123 GLU cc_start: 0.8437 (tp30) cc_final: 0.8145 (tp30) REVERT: A 130 GLU cc_start: 0.8033 (mp0) cc_final: 0.7747 (mp0) REVERT: A 196 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: A 199 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7892 (mtp85) REVERT: A 217 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: A 279 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 376 GLN cc_start: 0.8757 (tt0) cc_final: 0.8376 (tt0) REVERT: A 379 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 403 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7297 (mmm-85) REVERT: A 492 SER cc_start: 0.8524 (t) cc_final: 0.8274 (m) REVERT: B 25 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7871 (mm-40) REVERT: B 52 GLU cc_start: 0.8435 (tp30) cc_final: 0.7996 (tp30) REVERT: B 171 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.7935 (mtm-85) REVERT: B 271 GLU cc_start: 0.7866 (tp30) cc_final: 0.7480 (tp30) REVERT: B 279 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: B 302 GLU cc_start: 0.7821 (pm20) cc_final: 0.7462 (mp0) REVERT: B 315 ASP cc_start: 0.8541 (m-30) cc_final: 0.8273 (m-30) REVERT: B 430 ASP cc_start: 0.8309 (t0) cc_final: 0.8081 (t0) REVERT: B 517 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8740 (mmmt) REVERT: B 524 GLU cc_start: 0.7317 (pp20) cc_final: 0.7115 (pp20) REVERT: C 243 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7693 (t0) REVERT: C 308 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7663 (tp30) REVERT: C 312 ARG cc_start: 0.8311 (mmp80) cc_final: 0.8093 (mmp80) REVERT: C 430 ASP cc_start: 0.8358 (t0) cc_final: 0.7979 (t0) REVERT: C 461 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.7997 (m-70) REVERT: C 469 GLU cc_start: 0.8397 (tp30) cc_final: 0.8072 (mm-30) REVERT: C 525 GLN cc_start: 0.8372 (tp40) cc_final: 0.8135 (tp40) REVERT: C 526 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7330 (tm-30) REVERT: D 436 ASP cc_start: 0.7729 (t70) cc_final: 0.7511 (t0) REVERT: D 591 GLN cc_start: 0.8113 (tp40) cc_final: 0.7736 (tt0) REVERT: E 300 ILE cc_start: 0.8597 (mp) cc_final: 0.8349 (mp) REVERT: E 303 GLU cc_start: 0.7676 (pp20) cc_final: 0.7344 (pp20) REVERT: E 308 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7027 (mm-30) REVERT: E 329 ARG cc_start: 0.7823 (tmm-80) cc_final: 0.7481 (ttt90) REVERT: E 378 MET cc_start: 0.8617 (mtp) cc_final: 0.8172 (mtp) REVERT: E 383 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 497 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8104 (ttm-80) REVERT: E 507 GLU cc_start: 0.8755 (mt-10) cc_final: 0.7627 (mp0) REVERT: E 603 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: F 247 ASP cc_start: 0.8218 (m-30) cc_final: 0.7867 (m-30) REVERT: F 279 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7908 (mm-30) REVERT: F 313 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (mp) REVERT: F 383 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7803 (tm-30) REVERT: F 492 SER cc_start: 0.8694 (t) cc_final: 0.8451 (m) REVERT: F 507 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8208 (mt-10) outliers start: 69 outliers final: 41 residues processed: 546 average time/residue: 0.8010 time to fit residues: 483.6259 Evaluate side-chains 564 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 514 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 459 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 17 optimal weight: 0.1980 chunk 269 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 241 optimal weight: 0.0170 chunk 204 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 269 HIS A 282 ASN B 282 ASN C 554 GLN D 278 GLN D 316 ASN D 409 HIS D 525 GLN E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095670 restraints weight = 34017.004| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3110 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22280 Z= 0.129 Angle : 0.591 9.353 30424 Z= 0.299 Chirality : 0.041 0.174 3381 Planarity : 0.006 0.071 3955 Dihedral : 7.945 89.707 3284 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.34 % Favored : 96.33 % Rotamer: Outliers : 3.10 % Allowed : 21.23 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.33 (0.17), residues: 2726 helix: 1.93 (0.15), residues: 1311 sheet: -0.30 (0.29), residues: 328 loop : 0.06 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 385 TYR 0.010 0.001 TYR A 356 PHE 0.028 0.001 PHE B 59 TRP 0.044 0.001 TRP E 237 HIS 0.014 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (22262) covalent geometry : angle 0.59061 / 0.30 (30424) hydrogen bonds : bond 0.03577 / 2.36 ( 987) hydrogen bonds : angle 4.33282 / 3.14 ( 2778) metal coordination : bond 0.00236 / 0.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 521 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7808 (tt0) cc_final: 0.7527 (mt-10) REVERT: A 71 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.7258 (mtm-85) REVERT: A 113 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: A 130 GLU cc_start: 0.8037 (mp0) cc_final: 0.7767 (mp0) REVERT: A 182 SER cc_start: 0.8630 (m) cc_final: 0.8275 (p) REVERT: A 199 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7892 (mtp85) REVERT: A 217 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: A 279 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 376 GLN cc_start: 0.8752 (tt0) cc_final: 0.8349 (tt0) REVERT: A 379 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 492 SER cc_start: 0.8533 (t) cc_final: 0.8286 (m) REVERT: A 495 LEU cc_start: 0.8572 (tp) cc_final: 0.8323 (tp) REVERT: B 25 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7860 (mm-40) REVERT: B 52 GLU cc_start: 0.8439 (tp30) cc_final: 0.8005 (tp30) REVERT: B 68 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B 171 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7893 (mtm-85) REVERT: B 271 GLU cc_start: 0.7842 (tp30) cc_final: 0.7450 (tp30) REVERT: B 279 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: B 282 ASN cc_start: 0.8621 (m-40) cc_final: 0.8412 (m-40) REVERT: B 302 GLU cc_start: 0.7847 (pm20) cc_final: 0.7489 (mp0) REVERT: B 315 ASP cc_start: 0.8519 (m-30) cc_final: 0.8237 (m-30) REVERT: B 430 ASP cc_start: 0.8320 (t0) cc_final: 0.8083 (t0) REVERT: B 517 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8742 (mmmt) REVERT: B 524 GLU cc_start: 0.7306 (pp20) cc_final: 0.7037 (pp20) REVERT: C 243 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7696 (t0) REVERT: C 308 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7650 (tp30) REVERT: C 430 ASP cc_start: 0.8405 (t0) cc_final: 0.8003 (t0) REVERT: C 461 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7984 (m-70) REVERT: C 469 GLU cc_start: 0.8373 (tp30) cc_final: 0.8064 (mm-30) REVERT: C 525 GLN cc_start: 0.8399 (tp40) cc_final: 0.8164 (tp40) REVERT: C 526 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 333 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8022 (mmm160) REVERT: D 436 ASP cc_start: 0.7687 (t70) cc_final: 0.7470 (t0) REVERT: D 525 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: D 534 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8277 (mtp85) REVERT: D 591 GLN cc_start: 0.8107 (tp40) cc_final: 0.7725 (tt0) REVERT: E 300 ILE cc_start: 0.8591 (mp) cc_final: 0.8351 (mp) REVERT: E 303 GLU cc_start: 0.7685 (pp20) cc_final: 0.7371 (pp20) REVERT: E 308 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 329 ARG cc_start: 0.7829 (tmm-80) cc_final: 0.7466 (ttt90) REVERT: E 378 MET cc_start: 0.8604 (mtp) cc_final: 0.8165 (mtp) REVERT: E 383 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7914 (tm-30) REVERT: E 497 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8131 (ttm-80) REVERT: E 507 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7597 (mp0) REVERT: E 523 GLU cc_start: 0.7511 (tt0) cc_final: 0.7262 (mt-10) REVERT: E 603 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: F 247 ASP cc_start: 0.8184 (m-30) cc_final: 0.7835 (m-30) REVERT: F 279 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 313 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8619 (mp) REVERT: F 383 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 492 SER cc_start: 0.8669 (t) cc_final: 0.8454 (m) REVERT: F 507 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8180 (mt-10) outliers start: 69 outliers final: 38 residues processed: 553 average time/residue: 0.7800 time to fit residues: 477.5092 Evaluate side-chains 563 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 515 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 182 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 243 optimal weight: 0.0870 chunk 96 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 159 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 269 HIS A 282 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN D 278 GLN D 316 ASN D 372 ASN D 409 HIS ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095533 restraints weight = 34341.247| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.03 r_work: 0.3112 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 22280 Z= 0.170 Angle : 0.742 59.172 30424 Z= 0.404 Chirality : 0.041 0.178 3381 Planarity : 0.005 0.068 3955 Dihedral : 7.940 89.761 3284 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.52 % Favored : 96.18 % Rotamer: Outliers : 2.47 % Allowed : 22.17 % Favored : 75.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.11 % 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: 1.33 (0.17), residues: 2726 helix: 1.93 (0.15), residues: 1311 sheet: -0.30 (0.29), residues: 328 loop : 0.06 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 160 TYR 0.008 0.001 TYR F 336 PHE 0.026 0.001 PHE B 59 TRP 0.039 0.001 TRP E 237 HIS 0.016 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (22262) covalent geometry : angle 0.74182 / 0.40 (30424) hydrogen bonds : bond 0.03599 / 2.38 ( 987) hydrogen bonds : angle 4.33679 / 3.14 ( 2778) metal coordination : bond 0.00253 / 0.13 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5452 Ramachandran restraints generated. 2726 Oldfield, 0 Emsley, 2726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 512 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7756 (tt0) cc_final: 0.7459 (mt-10) REVERT: A 71 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7264 (mtm-85) REVERT: A 113 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: A 130 GLU cc_start: 0.8004 (mp0) cc_final: 0.7725 (mp0) REVERT: A 182 SER cc_start: 0.8633 (m) cc_final: 0.8277 (p) REVERT: A 199 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7902 (mtp85) REVERT: A 217 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: A 279 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 376 GLN cc_start: 0.8668 (tt0) cc_final: 0.8297 (tt0) REVERT: A 379 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 492 SER cc_start: 0.8533 (t) cc_final: 0.8285 (m) REVERT: B 25 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7859 (mm-40) REVERT: B 52 GLU cc_start: 0.8414 (tp30) cc_final: 0.7999 (tp30) REVERT: B 68 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 171 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7921 (mtm-85) REVERT: B 271 GLU cc_start: 0.7778 (tp30) cc_final: 0.7402 (tp30) REVERT: B 279 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: B 302 GLU cc_start: 0.7864 (pm20) cc_final: 0.7506 (mp0) REVERT: B 315 ASP cc_start: 0.8572 (m-30) cc_final: 0.8290 (m-30) REVERT: B 430 ASP cc_start: 0.8320 (t0) cc_final: 0.8083 (t0) REVERT: B 517 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8716 (mmmt) REVERT: B 524 GLU cc_start: 0.7310 (pp20) cc_final: 0.7095 (pp20) REVERT: C 243 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 308 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7676 (tp30) REVERT: C 430 ASP cc_start: 0.8411 (t0) cc_final: 0.7998 (t0) REVERT: C 461 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7995 (m-70) REVERT: C 469 GLU cc_start: 0.8336 (tp30) cc_final: 0.8041 (mm-30) REVERT: C 525 GLN cc_start: 0.8323 (tp40) cc_final: 0.8091 (tp40) REVERT: C 526 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 333 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7991 (mmm160) REVERT: D 369 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 380 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 436 ASP cc_start: 0.7665 (t70) cc_final: 0.7450 (t0) REVERT: D 507 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8306 (mt-10) REVERT: D 534 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8269 (mtp85) REVERT: D 591 GLN cc_start: 0.8097 (tp40) cc_final: 0.7712 (tt0) REVERT: D 593 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8277 (mt-10) REVERT: E 300 ILE cc_start: 0.8567 (mp) cc_final: 0.8328 (mp) REVERT: E 303 GLU cc_start: 0.7708 (pp20) cc_final: 0.7397 (pp20) REVERT: E 308 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7059 (mm-30) REVERT: E 329 ARG cc_start: 0.7837 (tmm-80) cc_final: 0.7464 (ttt90) REVERT: E 378 MET cc_start: 0.8617 (mtp) cc_final: 0.8183 (mtp) REVERT: E 383 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7914 (tm-30) REVERT: E 497 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8118 (ttm-80) REVERT: E 507 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7679 (mp0) REVERT: E 523 GLU cc_start: 0.7564 (tt0) cc_final: 0.7335 (mt-10) REVERT: E 603 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: F 247 ASP cc_start: 0.8203 (m-30) cc_final: 0.7842 (m-30) REVERT: F 279 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7892 (mm-30) REVERT: F 313 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8592 (mp) REVERT: F 383 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7844 (tm-30) REVERT: F 492 SER cc_start: 0.8653 (t) cc_final: 0.8437 (m) REVERT: F 580 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7625 (mp-120) outliers start: 55 outliers final: 40 residues processed: 536 average time/residue: 0.8878 time to fit residues: 524.3731 Evaluate side-chains 559 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 509 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 TRP Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 509 CYS Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 461 HIS Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 601 LEU Chi-restraints excluded: chain E residue 603 GLN Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 156 optimal weight: 0.2980 chunk 117 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS A 269 HIS A 282 ASN B 282 ASN C 554 GLN D 278 GLN D 316 ASN D 409 HIS E 234 HIS E 252 GLN E 355 ASN E 554 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095819 restraints weight = 34168.087| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.99 r_work: 0.3100 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22280 Z= 0.158 Angle : 0.613 9.654 30424 Z= 0.310 Chirality : 0.041 0.148 3381 Planarity : 0.006 0.059 3955 Dihedral : 7.899 89.650 3284 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.56 % Favored : 96.11 % Rotamer: Outliers : 2.47 % Allowed : 22.22 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.32 (0.17), residues: 2726 helix: 1.92 (0.14), residues: 1308 sheet: -0.33 (0.29), residues: 330 loop : 0.07 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 385 TYR 0.009 0.001 TYR F 336 PHE 0.032 0.001 PHE B 59 TRP 0.043 0.001 TRP E 237 HIS 0.017 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (22262) covalent geometry : angle 0.61324 / 0.31 (30424) hydrogen bonds : bond 0.03749 / 2.48 ( 987) hydrogen bonds : angle 4.34198 / 3.14 ( 2778) metal coordination : bond 0.00308 / 0.16 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9636.60 seconds wall clock time: 164 minutes 10.52 seconds (9850.52 seconds total)