Starting phenix.real_space_refine on Mon Oct 26 16:35:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx6_48711/10_2026/9mx6_48711.map" } resolution = 2.84 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= 0.004 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 13564 2.51 5 N 3565 2.21 5 O 4117 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4427 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 531} Chain breaks: 4 Chain: "B" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3716 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Chain breaks: 6 Chain: "C" Number of atoms: 4256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4256 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 509} Chain breaks: 5 Chain: "D" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4435 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 3 Chain: "E" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4442 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 3 Time building chain proxies: 4.83, per 1000 atoms: 0.23 Number of scatterers: 21276 At special positions: 0 Unit cell: (125.56, 129.86, 147.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 4117 8.00 N 3565 7.00 C 13564 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: 1.84 Conformation dependent library (CDL) restraints added in 922.5 milliseconds 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 11 sheets defined 41.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.663A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.558A pdb=" N ASN A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.596A pdb=" N ASP A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.621A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.824A pdb=" N PHE A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.128A pdb=" N ILE A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.640A pdb=" N VAL A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.860A pdb=" N ASP A 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 387 through 412 removed outlier: 3.726A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.584A pdb=" N LEU A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.609A pdb=" N ASN A 509 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 511 " --> pdb=" O THR A 508 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.851A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.617A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 204 through 208 removed outlier: 4.067A pdb=" N LEU B 208 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.991A pdb=" N LEU B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 270 through 282 removed outlier: 4.921A pdb=" N TYR B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 409 removed outlier: 3.983A pdb=" N CYS B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 4.260A pdb=" N TYR B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.572A pdb=" N LYS B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 507 through 514 removed outlier: 3.702A pdb=" N LEU B 510 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 511 " --> pdb=" O THR B 508 " (cutoff:3.500A) Proline residue: B 512 - end of helix No H-bonds generated for 'chain 'B' and resid 507 through 514' Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.535A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.838A pdb=" N LYS C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.876A pdb=" N THR C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.123A pdb=" N LEU C 208 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 235 through 250 removed outlier: 3.661A pdb=" N PHE C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.715A pdb=" N GLU C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.539A pdb=" N LEU C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 387 through 412 removed outlier: 3.576A pdb=" N CYS C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 431 Processing helix chain 'C' and resid 440 through 458 removed outlier: 3.543A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.775A pdb=" N ASN C 509 " --> pdb=" O ASP C 506 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 510 " --> pdb=" O ILE C 507 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 511 " --> pdb=" O THR C 508 " (cutoff:3.500A) Proline residue: C 512 - end of helix No H-bonds generated for 'chain 'C' and resid 506 through 514' Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.768A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.831A pdb=" N LYS D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.690A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.738A pdb=" N LYS D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.715A pdb=" N ASP D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 removed outlier: 3.654A pdb=" N LEU D 214 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.691A pdb=" N LYS D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.575A pdb=" N LYS D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 258' Processing helix chain 'D' and resid 270 through 282 removed outlier: 3.606A pdb=" N ARG D 280 " --> pdb=" O TYR D 276 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D 281 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.735A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 357 through 367 removed outlier: 3.560A pdb=" N ILE D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 411 removed outlier: 3.604A pdb=" N ILE D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 Processing helix chain 'D' and resid 440 through 458 removed outlier: 6.020A pdb=" N ARG D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.556A pdb=" N LEU D 499 " --> pdb=" O TYR D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.757A pdb=" N LEU D 511 " --> pdb=" O THR D 508 " (cutoff:3.500A) Proline residue: D 512 - end of helix Processing helix chain 'D' and resid 547 through 554 removed outlier: 3.910A pdb=" N LYS D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.631A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.726A pdb=" N LYS E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 233 through 249 removed outlier: 3.794A pdb=" N VAL E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 260 removed outlier: 3.539A pdb=" N GLU E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 removed outlier: 3.543A pdb=" N VAL E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.511A pdb=" N PHE E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.784A pdb=" N SER E 355 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 366 Processing helix chain 'E' and resid 387 through 407 removed outlier: 3.586A pdb=" N CYS E 391 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 Processing helix chain 'E' and resid 440 through 458 removed outlier: 5.608A pdb=" N ARG E 455 " --> pdb=" O ALA E 451 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'E' and resid 507 through 514 removed outlier: 3.829A pdb=" N LEU E 511 " --> pdb=" O THR E 508 " (cutoff:3.500A) Proline residue: E 512 - end of helix Processing helix chain 'E' and resid 547 through 553 Processing helix chain 'E' and resid 560 through 570 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.574A pdb=" N LYS A 20 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL A 14 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 23 current: chain 'A' and resid 50 through 62 removed outlier: 6.927A pdb=" N ALA A 51 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU A 80 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 53 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 74 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 59 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET A 72 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE A 61 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS A 70 " --> pdb=" O ILE A 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 88 current: chain 'B' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 23 current: chain 'B' and resid 50 through 60 removed outlier: 7.046A pdb=" N ALA B 51 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU B 80 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 53 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU B 74 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 59 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET B 72 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 138 removed outlier: 4.719A pdb=" N SER A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 137 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 123 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 185 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU A 426 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 187 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN A 201 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP A 379 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 203 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.817A pdb=" N SER B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL B 137 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR B 123 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 530 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 148 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLU B 426 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE B 187 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 201 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASP B 379 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 203 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.670A pdb=" N LYS C 20 " --> pdb=" O VAL C 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 23 current: chain 'C' and resid 52 through 60 removed outlier: 7.119A pdb=" N LEU C 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU C 74 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 59 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET C 72 " --> pdb=" O PHE C 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 87 current: chain 'D' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 23 current: chain 'D' and resid 50 through 62 removed outlier: 7.188A pdb=" N ALA D 51 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D 80 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU D 53 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU D 74 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE D 59 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET D 72 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE D 61 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS D 70 " --> pdb=" O ILE D 61 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 86 through 88 current: chain 'E' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 7.075A pdb=" N ALA E 51 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU E 80 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU E 53 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU E 74 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE E 59 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET E 72 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE E 61 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS E 70 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 134 through 138 removed outlier: 4.444A pdb=" N SER C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL C 137 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR C 123 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 148 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE C 187 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 184 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU C 378 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 186 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 201 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP C 379 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU C 203 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 299 through 301 removed outlier: 3.721A pdb=" N THR C 316 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 134 through 138 removed outlier: 4.593A pdb=" N SER D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL D 137 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR D 123 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA D 148 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP D 379 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 203 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB1, first strand: chain 'E' and resid 134 through 138 removed outlier: 4.737A pdb=" N SER E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 137 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR E 123 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA E 148 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN E 201 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP E 379 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 203 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 298 through 301 740 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5597 1.33 - 1.45: 3605 1.45 - 1.57: 12417 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 21664 Sorted by residual: bond pdb=" N ILE C 7 " pdb=" CA ILE C 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N ILE A 7 " pdb=" CA ILE A 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ILE E 7 " pdb=" CA ILE E 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N ILE D 7 " pdb=" CA ILE D 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 ... (remaining 21659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 28685 1.60 - 3.20: 482 3.20 - 4.81: 56 4.81 - 6.41: 8 6.41 - 8.01: 3 Bond angle restraints: 29234 Sorted by residual: angle pdb=" CA TRP C 552 " pdb=" CB TRP C 552 " pdb=" CG TRP C 552 " ideal model delta sigma weight residual 113.60 121.61 -8.01 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CA GLU B 107 " pdb=" CB GLU B 107 " pdb=" CG GLU B 107 " ideal model delta sigma weight residual 114.10 106.49 7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB GLU B 107 " pdb=" CG GLU B 107 " pdb=" CD GLU B 107 " ideal model delta sigma weight residual 112.60 107.25 5.35 1.70e+00 3.46e-01 9.89e+00 angle pdb=" CA ILE A 528 " pdb=" C ILE A 528 " pdb=" N PRO A 529 " ideal model delta sigma weight residual 116.57 119.10 -2.53 9.80e-01 1.04e+00 6.69e+00 angle pdb=" N PRO A 96 " pdb=" CA PRO A 96 " pdb=" C PRO A 96 " ideal model delta sigma weight residual 110.70 113.84 -3.14 1.22e+00 6.72e-01 6.63e+00 ... (remaining 29229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 12001 16.48 - 32.96: 982 32.96 - 49.43: 170 49.43 - 65.91: 58 65.91 - 82.39: 7 Dihedral angle restraints: 13218 sinusoidal: 5452 harmonic: 7766 Sorted by residual: dihedral pdb=" CA PRO A 96 " pdb=" C PRO A 96 " pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN E 278 " pdb=" C ASN E 278 " pdb=" N ASN E 279 " pdb=" CA ASN E 279 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA LYS C 287 " pdb=" C LYS C 287 " pdb=" N ASP C 288 " pdb=" CA ASP C 288 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 13215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1984 0.032 - 0.063: 876 0.063 - 0.095: 214 0.095 - 0.127: 192 0.127 - 0.159: 31 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CA ILE D 531 " pdb=" N ILE D 531 " pdb=" C ILE D 531 " pdb=" CB ILE D 531 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA ILE E 7 " pdb=" N ILE E 7 " pdb=" C ILE E 7 " pdb=" CB ILE E 7 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE E 61 " pdb=" N ILE E 61 " pdb=" C ILE E 61 " pdb=" CB ILE E 61 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3294 not shown) Planarity restraints: 3754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 107 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" CD GLU B 107 " 0.074 2.00e-02 2.50e+03 pdb=" OE1 GLU B 107 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU B 107 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 96 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 97 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 280 " -0.183 9.50e-02 1.11e+02 8.23e-02 4.93e+00 pdb=" NE ARG C 280 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 280 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 280 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 280 " -0.001 2.00e-02 2.50e+03 ... (remaining 3751 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 135 2.56 - 3.14: 16462 3.14 - 3.73: 29128 3.73 - 4.31: 42297 4.31 - 4.90: 72356 Nonbonded interactions: 160378 Sorted by model distance: nonbonded pdb=" OG SER E 294 " pdb=" OD2 ASP E 318 " model vdw 1.975 3.040 nonbonded pdb=" OE2 GLU A 221 " pdb=" NH1 ARG A 235 " model vdw 2.023 3.120 nonbonded pdb=" O HIS A 232 " pdb=" ND2 ASN A 236 " model vdw 2.135 3.120 nonbonded pdb=" ND2 ASN C 8 " pdb=" OE2 GLU C 28 " model vdw 2.138 3.120 nonbonded pdb=" OD1 ASN D 204 " pdb=" OD1 ASP D 206 " model vdw 2.147 3.040 ... (remaining 160373 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 7 through 29 or resid 36 through 44 or resid 50 through 61 \ or resid 70 through 88 or resid 97 through 225 or resid 234 through 411 or resi \ d 417 through 571)) selection = (chain 'C' and (resid 7 through 312 or resid 316 through 411 or resid 417 throug \ h 540 or resid 545 through 571)) selection = (chain 'D' and (resid 7 through 29 or resid 36 through 44 or resid 50 through 61 \ or resid 70 through 88 or resid 97 through 225 or resid 234 through 312 or resi \ d 316 through 411 or resid 417 through 540 or resid 545 through 571)) selection = (chain 'E' and (resid 7 through 29 or resid 36 through 44 or resid 50 through 61 \ or resid 70 through 88 or resid 97 through 225 or resid 234 through 312 or resi \ d 316 through 540 or resid 545 through 571)) } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.410 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.003 0.056 21664 Z= 0.115 Angle : 0.530 8.012 29234 Z= 0.287 Chirality : 0.044 0.159 3297 Planarity : 0.004 0.103 3754 Dihedral : 12.810 82.390 8172 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.16), residues: 2605 helix: 0.95 (0.18), residues: 848 sheet: -0.11 (0.25), residues: 448 loop : -1.17 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 280 TYR 0.031 0.001 TYR E 548 PHE 0.020 0.001 PHE A 385 TRP 0.035 0.002 TRP C 552 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (21664) covalent geometry : angle 0.53026 / 0.29 (29234) hydrogen bonds : bond 0.21911 / 14.02 ( 740) hydrogen bonds : angle 6.11264 / 4.22 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7519 (tp30) cc_final: 0.6987 (tp30) REVERT: B 76 SER cc_start: 0.8133 (m) cc_final: 0.7881 (p) REVERT: B 121 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7780 (mtt180) REVERT: C 170 ASP cc_start: 0.7041 (m-30) cc_final: 0.6802 (m-30) REVERT: C 260 ILE cc_start: 0.6660 (mt) cc_final: 0.6175 (mt) REVERT: C 269 ASP cc_start: 0.7545 (t70) cc_final: 0.7246 (t0) REVERT: C 407 LYS cc_start: 0.6358 (tptp) cc_final: 0.6132 (tptp) REVERT: C 426 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6824 (tm-30) REVERT: C 550 ASP cc_start: 0.6466 (m-30) cc_final: 0.6168 (m-30) REVERT: D 77 PRO cc_start: 0.8621 (Cg_endo) cc_final: 0.8377 (Cg_exo) REVERT: D 192 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6540 (mt-10) REVERT: D 246 LYS cc_start: 0.6399 (mttt) cc_final: 0.5532 (mttm) REVERT: D 379 ASP cc_start: 0.7269 (t70) cc_final: 0.7059 (t0) REVERT: D 453 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7958 (mt-10) REVERT: D 502 ASP cc_start: 0.6577 (t0) cc_final: 0.6308 (t0) REVERT: E 142 PHE cc_start: 0.7478 (t80) cc_final: 0.7170 (t80) REVERT: E 170 ASP cc_start: 0.7194 (m-30) cc_final: 0.6876 (m-30) outliers start: 0 outliers final: 3 residues processed: 366 average time/residue: 0.5957 time to fit residues: 248.8244 Evaluate side-chains 305 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 371 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 83 ASN A 279 ASN A 282 ASN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 166 GLN B 489 ASN C 166 GLN C 263 HIS C 289 ASN D 159 HIS D 245 ASN D 466 GLN E 159 HIS E 199 ASN E 263 HIS E 279 ASN E 480 ASN E 489 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.192018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161076 restraints weight = 29163.528| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.25 r_work: 0.3928 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21664 Z= 0.183 Angle : 0.633 10.511 29234 Z= 0.340 Chirality : 0.049 0.221 3297 Planarity : 0.005 0.104 3754 Dihedral : 5.081 64.657 2829 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.61 % Allowed : 8.44 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.40 (0.16), residues: 2605 helix: 1.09 (0.18), residues: 856 sheet: 0.19 (0.25), residues: 439 loop : -1.38 (0.15), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 553 TYR 0.027 0.002 TYR C 548 PHE 0.034 0.003 PHE D 268 TRP 0.014 0.002 TRP D 552 HIS 0.007 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (21664) covalent geometry : angle 0.63347 / 0.34 (29234) hydrogen bonds : bond 0.05397 / 3.50 ( 740) hydrogen bonds : angle 4.60184 / 3.13 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 340 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7507 (pt) REVERT: A 131 THR cc_start: 0.8461 (p) cc_final: 0.8256 (m) REVERT: A 141 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.8066 (mmm-85) REVERT: A 144 ASN cc_start: 0.7896 (p0) cc_final: 0.7693 (p0) REVERT: A 191 SER cc_start: 0.8225 (m) cc_final: 0.7656 (m) REVERT: A 386 GLU cc_start: 0.7035 (pm20) cc_final: 0.6411 (pm20) REVERT: A 394 LEU cc_start: 0.8005 (tp) cc_final: 0.7735 (tp) REVERT: A 485 MET cc_start: 0.8343 (mmm) cc_final: 0.8049 (mmt) REVERT: C 188 ASP cc_start: 0.7341 (m-30) cc_final: 0.7049 (m-30) REVERT: C 305 GLU cc_start: 0.6467 (tp30) cc_final: 0.6053 (mp0) REVERT: C 445 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 129 LEU cc_start: 0.7816 (mt) cc_final: 0.7556 (mt) REVERT: D 192 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7148 (mt-10) REVERT: D 246 LYS cc_start: 0.6448 (mttt) cc_final: 0.5476 (mttm) REVERT: D 404 TYR cc_start: 0.6763 (t80) cc_final: 0.6559 (t80) REVERT: D 455 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7874 (mtp180) REVERT: D 536 LYS cc_start: 0.8221 (ptmm) cc_final: 0.7992 (ttpp) REVERT: E 426 GLU cc_start: 0.7649 (mp0) cc_final: 0.7388 (mp0) REVERT: E 449 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7819 (ttp-170) outliers start: 39 outliers final: 16 residues processed: 358 average time/residue: 0.5911 time to fit residues: 241.7181 Evaluate side-chains 314 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 297 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [181, 191, 22, 67, 259, 136, 5, 245, 164, 123, 14] chunk 181 optimal weight: 0.0770 chunk 191 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 245 optimal weight: 0.0670 chunk 164 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 130 ASN A 281 ASN B 144 ASN B 466 GLN B 489 ASN C 166 GLN D 183 HIS D 195 ASN E 166 GLN E 199 ASN E 271 ASN E 429 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161466 restraints weight = 29253.659| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.33 r_work: 0.3928 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21664 Z= 0.107 Angle : 0.509 11.698 29234 Z= 0.275 Chirality : 0.045 0.325 3297 Planarity : 0.004 0.098 3754 Dihedral : 4.373 31.469 2822 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 10.34 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.09 (0.16), residues: 2605 helix: 1.43 (0.19), residues: 857 sheet: 0.37 (0.25), residues: 438 loop : -1.26 (0.15), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 280 TYR 0.016 0.001 TYR C 212 PHE 0.031 0.002 PHE A 385 TRP 0.011 0.001 TRP E 213 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (21664) covalent geometry : angle 0.50946 / 0.27 (29234) hydrogen bonds : bond 0.03996 / 2.58 ( 740) hydrogen bonds : angle 4.24739 / 2.89 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7343 (pt) REVERT: A 222 GLU cc_start: 0.7485 (tp30) cc_final: 0.6982 (tp30) REVERT: A 267 TYR cc_start: 0.6586 (t80) cc_final: 0.6320 (t80) REVERT: A 386 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: A 394 LEU cc_start: 0.7748 (tp) cc_final: 0.7481 (tp) REVERT: C 305 GLU cc_start: 0.6444 (tp30) cc_final: 0.5979 (mp0) REVERT: C 368 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.4767 (m-80) REVERT: C 530 SER cc_start: 0.8393 (t) cc_final: 0.8032 (m) REVERT: D 77 PRO cc_start: 0.8603 (Cg_endo) cc_final: 0.8339 (Cg_exo) REVERT: D 129 LEU cc_start: 0.7670 (mt) cc_final: 0.7395 (mt) REVERT: D 246 LYS cc_start: 0.6287 (mttt) cc_final: 0.5880 (mttp) REVERT: D 280 ARG cc_start: 0.6754 (ttm110) cc_final: 0.6488 (ttm170) REVERT: D 455 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7770 (mtp180) REVERT: E 426 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: E 449 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7419 (ttp-170) outliers start: 54 outliers final: 17 residues processed: 348 average time/residue: 0.5467 time to fit residues: 218.5307 Evaluate side-chains 316 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 295 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 426 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [19, 138, 145, 235, 102, 117, 184, 245, 34, 46, 120] chunk 19 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 117 optimal weight: 0.0370 chunk 184 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN B 466 GLN C 308 HIS D 281 ASN E 199 ASN E 275 ASN E 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.190257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158564 restraints weight = 29185.354| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.31 r_work: 0.3889 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21664 Z= 0.136 Angle : 0.544 11.344 29234 Z= 0.291 Chirality : 0.045 0.307 3297 Planarity : 0.004 0.101 3754 Dihedral : 4.400 33.650 2822 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.19 % Allowed : 12.32 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.12 (0.16), residues: 2605 helix: 1.37 (0.19), residues: 861 sheet: 0.33 (0.25), residues: 442 loop : -1.26 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 280 TYR 0.018 0.002 TYR C 212 PHE 0.028 0.002 PHE A 561 TRP 0.015 0.002 TRP E 213 HIS 0.006 0.001 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21664) covalent geometry : angle 0.54367 / 0.29 (29234) hydrogen bonds : bond 0.04542 / 2.94 ( 740) hydrogen bonds : angle 4.26529 / 2.89 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8524 (mtmm) REVERT: A 23 VAL cc_start: 0.7850 (t) cc_final: 0.7643 (m) REVERT: A 222 GLU cc_start: 0.7819 (tp30) cc_final: 0.7279 (tp30) REVERT: A 248 ILE cc_start: 0.7157 (mt) cc_final: 0.6914 (mt) REVERT: A 386 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6204 (pm20) REVERT: A 394 LEU cc_start: 0.7956 (tp) cc_final: 0.7717 (tp) REVERT: A 485 MET cc_start: 0.8206 (mmm) cc_final: 0.7993 (mmt) REVERT: A 535 GLU cc_start: 0.7229 (pt0) cc_final: 0.6971 (mt-10) REVERT: B 397 ARG cc_start: 0.6411 (ttm110) cc_final: 0.6062 (ttp80) REVERT: C 20 LYS cc_start: 0.6476 (mppt) cc_final: 0.6248 (mppt) REVERT: C 305 GLU cc_start: 0.6595 (tp30) cc_final: 0.6070 (mp0) REVERT: C 368 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.5793 (t80) REVERT: C 445 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 246 LYS cc_start: 0.6358 (mttt) cc_final: 0.5976 (mttp) REVERT: D 360 GLU cc_start: 0.6255 (mt-10) cc_final: 0.6010 (mt-10) REVERT: D 362 LEU cc_start: 0.7696 (mm) cc_final: 0.7452 (mm) REVERT: D 455 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7848 (mtp180) REVERT: E 185 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8245 (mt) REVERT: E 187 PHE cc_start: 0.8507 (m-80) cc_final: 0.8265 (m-80) REVERT: E 426 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: E 449 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7742 (ttp-170) outliers start: 53 outliers final: 22 residues processed: 324 average time/residue: 0.5592 time to fit residues: 208.4067 Evaluate side-chains 309 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 426 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [257, 25, 189, 43, 244, 132, 233, 229, 195, 143, 11] chunk 257 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 189 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 229 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 GLN C 567 GLN D 275 ASN E 166 GLN E 199 ASN E 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.192058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160407 restraints weight = 29239.292| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.38 r_work: 0.3911 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21664 Z= 0.092 Angle : 0.486 12.209 29234 Z= 0.259 Chirality : 0.044 0.308 3297 Planarity : 0.004 0.097 3754 Dihedral : 4.109 31.154 2822 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.90 % Allowed : 13.94 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: 0.05 (0.16), residues: 2605 helix: 1.57 (0.19), residues: 867 sheet: 0.40 (0.26), residues: 435 loop : -1.19 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 467 TYR 0.014 0.001 TYR C 212 PHE 0.020 0.001 PHE A 385 TRP 0.011 0.001 TRP E 213 HIS 0.005 0.001 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (21664) covalent geometry : angle 0.48627 / 0.26 (29234) hydrogen bonds : bond 0.03389 / 2.19 ( 740) hydrogen bonds : angle 4.08818 / 2.77 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8459 (mtmm) REVERT: A 222 GLU cc_start: 0.7505 (tp30) cc_final: 0.6989 (tp30) REVERT: A 248 ILE cc_start: 0.7118 (mt) cc_final: 0.6847 (mt) REVERT: A 386 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5965 (pm20) REVERT: A 394 LEU cc_start: 0.7796 (tp) cc_final: 0.7558 (tp) REVERT: A 485 MET cc_start: 0.7990 (mmm) cc_final: 0.7704 (mmt) REVERT: A 488 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 535 GLU cc_start: 0.6892 (pt0) cc_final: 0.6667 (mt-10) REVERT: B 58 ASN cc_start: 0.7317 (p0) cc_final: 0.7097 (p0) REVERT: B 181 ASN cc_start: 0.6629 (t0) cc_final: 0.5051 (t0) REVERT: B 397 ARG cc_start: 0.6124 (ttm110) cc_final: 0.5812 (ttp80) REVERT: B 489 ASN cc_start: 0.7830 (t0) cc_final: 0.7625 (t0) REVERT: C 20 LYS cc_start: 0.6417 (mppt) cc_final: 0.6154 (mppt) REVERT: C 305 GLU cc_start: 0.6419 (tp30) cc_final: 0.6053 (mp0) REVERT: C 368 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4902 (m-80) REVERT: C 445 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6903 (mm-30) REVERT: C 497 LYS cc_start: 0.7887 (mtpm) cc_final: 0.7670 (mtpp) REVERT: C 530 SER cc_start: 0.8412 (t) cc_final: 0.8123 (m) REVERT: D 77 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.8308 (Cg_exo) REVERT: D 207 THR cc_start: 0.7624 (p) cc_final: 0.7414 (m) REVERT: D 246 LYS cc_start: 0.6256 (mttt) cc_final: 0.5172 (tttm) REVERT: D 280 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6547 (ttm110) REVERT: D 455 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7702 (mtp180) REVERT: E 187 PHE cc_start: 0.8409 (m-80) cc_final: 0.8168 (m-80) REVERT: E 426 GLU cc_start: 0.7314 (mp0) cc_final: 0.7113 (mp0) REVERT: E 449 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7646 (ttp-110) outliers start: 46 outliers final: 22 residues processed: 310 average time/residue: 0.5608 time to fit residues: 199.9521 Evaluate side-chains 306 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [89, 160, 68, 192, 251, 166, 247, 56, 73, 45, 30] chunk 89 optimal weight: 9.9990 chunk 160 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN B 466 GLN C 166 GLN C 183 HIS D 275 ASN E 166 GLN E 480 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154143 restraints weight = 28868.124| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.36 r_work: 0.3835 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21664 Z= 0.226 Angle : 0.646 10.863 29234 Z= 0.346 Chirality : 0.049 0.313 3297 Planarity : 0.005 0.103 3754 Dihedral : 4.776 34.412 2822 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.48 % Allowed : 14.14 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.40 (0.16), residues: 2605 helix: 1.13 (0.19), residues: 840 sheet: 0.16 (0.25), residues: 434 loop : -1.37 (0.15), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 467 TYR 0.022 0.002 TYR E 495 PHE 0.038 0.003 PHE A 385 TRP 0.023 0.003 TRP E 213 HIS 0.008 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (21664) covalent geometry : angle 0.64559 / 0.35 (29234) hydrogen bonds : bond 0.05814 / 3.79 ( 740) hydrogen bonds : angle 4.56193 / 3.10 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7752 (tp30) cc_final: 0.7260 (tp30) REVERT: A 470 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: A 488 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7795 (t) REVERT: A 535 GLU cc_start: 0.7312 (pt0) cc_final: 0.6998 (mt-10) REVERT: B 189 ILE cc_start: 0.7255 (pt) cc_final: 0.7044 (mt) REVERT: B 199 ASN cc_start: 0.5874 (p0) cc_final: 0.5611 (t0) REVERT: B 262 PHE cc_start: 0.7027 (t80) cc_final: 0.6714 (t80) REVERT: B 489 ASN cc_start: 0.8000 (t0) cc_final: 0.7666 (t0) REVERT: C 20 LYS cc_start: 0.6804 (mppt) cc_final: 0.6514 (mppt) REVERT: C 238 PHE cc_start: 0.4189 (OUTLIER) cc_final: 0.3269 (t80) REVERT: C 305 GLU cc_start: 0.6533 (tp30) cc_final: 0.6167 (mp0) REVERT: C 368 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5584 (t80) REVERT: C 445 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 497 LYS cc_start: 0.8102 (mtpm) cc_final: 0.7874 (mtpp) REVERT: D 18 LYS cc_start: 0.7476 (ttpt) cc_final: 0.7274 (mtpt) REVERT: D 43 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7162 (ttt-90) REVERT: D 129 LEU cc_start: 0.7796 (mt) cc_final: 0.7535 (mt) REVERT: D 246 LYS cc_start: 0.6521 (mttt) cc_final: 0.6131 (tttt) REVERT: D 280 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7207 (ttm110) REVERT: D 360 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5989 (mt-10) REVERT: D 455 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7912 (mtp180) REVERT: E 91 ASP cc_start: 0.7586 (t0) cc_final: 0.7302 (t70) REVERT: E 449 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7682 (mtm-85) outliers start: 60 outliers final: 31 residues processed: 346 average time/residue: 0.5708 time to fit residues: 226.1660 Evaluate side-chains 336 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [3, 96, 170, 112, 154, 65, 82, 165, 17, 9, 59] chunk 3 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 0.0670 chunk 165 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 466 GLN B 166 GLN B 466 GLN C 166 GLN E 166 GLN E 199 ASN E 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.188981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.158147 restraints weight = 29123.366| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.28 r_work: 0.3894 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21664 Z= 0.095 Angle : 0.504 9.499 29234 Z= 0.270 Chirality : 0.044 0.307 3297 Planarity : 0.004 0.097 3754 Dihedral : 4.242 31.170 2822 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.45 % Allowed : 16.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.11 (0.16), residues: 2605 helix: 1.45 (0.19), residues: 864 sheet: 0.19 (0.25), residues: 444 loop : -1.25 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 280 TYR 0.014 0.001 TYR C 212 PHE 0.031 0.001 PHE A 385 TRP 0.012 0.001 TRP E 213 HIS 0.005 0.001 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (21664) covalent geometry : angle 0.50410 / 0.27 (29234) hydrogen bonds : bond 0.03517 / 2.27 ( 740) hydrogen bonds : angle 4.19903 / 2.85 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8070 (m) cc_final: 0.7859 (m) REVERT: A 222 GLU cc_start: 0.7781 (tp30) cc_final: 0.7231 (tp30) REVERT: A 386 GLU cc_start: 0.7049 (pm20) cc_final: 0.6409 (pm20) REVERT: A 485 MET cc_start: 0.8177 (mmm) cc_final: 0.7927 (mmt) REVERT: A 488 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7717 (t) REVERT: A 535 GLU cc_start: 0.7219 (pt0) cc_final: 0.6908 (mt-10) REVERT: B 166 GLN cc_start: 0.7873 (tp40) cc_final: 0.7387 (tp40) REVERT: B 199 ASN cc_start: 0.5977 (p0) cc_final: 0.5730 (t0) REVERT: B 397 ARG cc_start: 0.6220 (ttm110) cc_final: 0.5395 (ttp-170) REVERT: C 20 LYS cc_start: 0.6835 (mppt) cc_final: 0.6482 (mppt) REVERT: C 305 GLU cc_start: 0.6441 (tp30) cc_final: 0.6133 (mp0) REVERT: C 368 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5669 (t80) REVERT: C 497 LYS cc_start: 0.8038 (mtpm) cc_final: 0.7816 (mtpp) REVERT: C 530 SER cc_start: 0.8503 (t) cc_final: 0.8260 (m) REVERT: D 246 LYS cc_start: 0.6451 (mttt) cc_final: 0.6026 (mttp) REVERT: D 280 ARG cc_start: 0.7351 (tpp80) cc_final: 0.7117 (ttm110) REVERT: D 455 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7816 (mtp180) REVERT: E 91 ASP cc_start: 0.7474 (t0) cc_final: 0.7223 (t70) REVERT: E 251 GLN cc_start: 0.7436 (mt0) cc_final: 0.6977 (tm-30) REVERT: E 449 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7733 (ttp-170) outliers start: 35 outliers final: 22 residues processed: 329 average time/residue: 0.5770 time to fit residues: 217.6698 Evaluate side-chains 325 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 439 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [73, 103, 106, 132, 56, 67, 164, 13, 19, 27, 205] chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 205 optimal weight: 0.2980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN B 466 GLN B 480 ASN B 494 ASN C 166 GLN D 190 HIS E 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.155018 restraints weight = 28833.349| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.30 r_work: 0.3846 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21664 Z= 0.180 Angle : 0.601 10.634 29234 Z= 0.321 Chirality : 0.047 0.304 3297 Planarity : 0.005 0.102 3754 Dihedral : 4.532 34.116 2822 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.78 % Allowed : 16.63 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: 2605 helix: 1.15 (0.19), residues: 866 sheet: 0.22 (0.26), residues: 420 loop : -1.34 (0.15), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 280 TYR 0.025 0.002 TYR B 87 PHE 0.033 0.002 PHE A 385 TRP 0.020 0.002 TRP E 213 HIS 0.007 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (21664) covalent geometry : angle 0.60102 / 0.32 (29234) hydrogen bonds : bond 0.05153 / 3.37 ( 740) hydrogen bonds : angle 4.45824 / 3.03 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7737 (tp30) cc_final: 0.7218 (tp30) REVERT: A 386 GLU cc_start: 0.7093 (pm20) cc_final: 0.6355 (pm20) REVERT: A 488 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 498 ARG cc_start: 0.8787 (ttp-110) cc_final: 0.8554 (ttt-90) REVERT: A 534 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7523 (mm) REVERT: A 535 GLU cc_start: 0.7313 (pt0) cc_final: 0.6976 (mt-10) REVERT: B 121 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7892 (mtt180) REVERT: B 189 ILE cc_start: 0.7205 (pt) cc_final: 0.6944 (mt) REVERT: B 397 ARG cc_start: 0.6275 (ttm110) cc_final: 0.5390 (ttp80) REVERT: B 449 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7782 (ttm170) REVERT: B 515 LYS cc_start: 0.7344 (mttt) cc_final: 0.7062 (mttt) REVERT: C 20 LYS cc_start: 0.6937 (mppt) cc_final: 0.6586 (mppt) REVERT: C 305 GLU cc_start: 0.6461 (tp30) cc_final: 0.6150 (mp0) REVERT: C 368 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5675 (t80) REVERT: C 497 LYS cc_start: 0.8108 (mtpm) cc_final: 0.7854 (mtpp) REVERT: D 31 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7743 (tp) REVERT: D 246 LYS cc_start: 0.6536 (mttt) cc_final: 0.6148 (mttp) REVERT: D 280 ARG cc_start: 0.7497 (tpp80) cc_final: 0.7174 (ttm110) REVERT: D 360 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5958 (mt-10) REVERT: D 455 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7874 (mtp180) REVERT: E 449 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7717 (ttp-170) outliers start: 43 outliers final: 24 residues processed: 337 average time/residue: 0.5863 time to fit residues: 225.4671 Evaluate side-chains 341 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 488 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [205, 181, 148, 231, 159, 191, 97, 172, 185, 67, 33] chunk 205 optimal weight: 2.9990 chunk 181 optimal weight: 0.0370 chunk 148 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 159 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN B 144 ASN B 199 ASN B 480 ASN B 494 ASN C 166 GLN E 166 GLN E 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154487 restraints weight = 28733.442| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.35 r_work: 0.3835 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21664 Z= 0.180 Angle : 0.601 10.112 29234 Z= 0.322 Chirality : 0.047 0.316 3297 Planarity : 0.005 0.098 3754 Dihedral : 4.605 33.242 2822 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.70 % Allowed : 16.83 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.46 (0.16), residues: 2605 helix: 1.04 (0.18), residues: 864 sheet: 0.10 (0.25), residues: 433 loop : -1.41 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 280 TYR 0.021 0.002 TYR E 495 PHE 0.033 0.002 PHE A 385 TRP 0.018 0.002 TRP E 213 HIS 0.007 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (21664) covalent geometry : angle 0.60127 / 0.32 (29234) hydrogen bonds : bond 0.04935 / 3.20 ( 740) hydrogen bonds : angle 4.48952 / 3.05 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7814 (tp30) cc_final: 0.7314 (tp30) REVERT: A 488 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7793 (t) REVERT: A 535 GLU cc_start: 0.7301 (pt0) cc_final: 0.6950 (mt-10) REVERT: B 121 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7863 (mtt180) REVERT: B 262 PHE cc_start: 0.7083 (t80) cc_final: 0.6867 (t80) REVERT: B 397 ARG cc_start: 0.6324 (ttm110) cc_final: 0.5427 (ttp80) REVERT: B 449 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7773 (ttm170) REVERT: B 515 LYS cc_start: 0.7379 (mttt) cc_final: 0.7096 (mttt) REVERT: C 20 LYS cc_start: 0.6942 (mppt) cc_final: 0.6591 (mppt) REVERT: C 60 SER cc_start: 0.7379 (p) cc_final: 0.6882 (m) REVERT: C 238 PHE cc_start: 0.4122 (OUTLIER) cc_final: 0.3330 (t80) REVERT: C 305 GLU cc_start: 0.6431 (tp30) cc_final: 0.6184 (mp0) REVERT: C 368 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5728 (t80) REVERT: C 448 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7305 (tp30) REVERT: C 497 LYS cc_start: 0.8158 (mtpm) cc_final: 0.7907 (mtpp) REVERT: D 31 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7758 (tp) REVERT: D 92 SER cc_start: 0.7654 (m) cc_final: 0.7258 (p) REVERT: D 246 LYS cc_start: 0.6559 (mttt) cc_final: 0.6232 (mttp) REVERT: D 280 ARG cc_start: 0.7516 (tpp80) cc_final: 0.7168 (ttm110) REVERT: D 360 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5966 (mt-10) REVERT: D 455 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7907 (mtp180) REVERT: E 449 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7906 (ttp-110) outliers start: 41 outliers final: 28 residues processed: 334 average time/residue: 0.5850 time to fit residues: 223.4830 Evaluate side-chains 333 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 488 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [53, 205, 91, 191, 257, 71, 194, 123, 221, 59, 6] chunk 53 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN C 166 GLN C 567 GLN D 138 ASN D 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154781 restraints weight = 28980.363| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.30 r_work: 0.3845 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21664 Z= 0.165 Angle : 0.593 10.014 29234 Z= 0.317 Chirality : 0.047 0.314 3297 Planarity : 0.005 0.102 3754 Dihedral : 4.560 34.137 2822 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.49 % Allowed : 17.25 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.42 (0.16), residues: 2605 helix: 1.08 (0.18), residues: 866 sheet: 0.07 (0.26), residues: 421 loop : -1.36 (0.15), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 280 TYR 0.021 0.002 TYR E 495 PHE 0.035 0.002 PHE A 385 TRP 0.019 0.002 TRP E 213 HIS 0.006 0.001 HIS D 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (21664) covalent geometry : angle 0.59278 / 0.32 (29234) hydrogen bonds : bond 0.04838 / 3.16 ( 740) hydrogen bonds : angle 4.46004 / 3.03 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7781 (tp30) cc_final: 0.7277 (tp30) REVERT: A 488 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7793 (t) REVERT: A 535 GLU cc_start: 0.7297 (pt0) cc_final: 0.6937 (mt-10) REVERT: B 121 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7858 (mtt180) REVERT: B 262 PHE cc_start: 0.7132 (t80) cc_final: 0.6918 (t80) REVERT: B 397 ARG cc_start: 0.6303 (ttm110) cc_final: 0.5418 (ttp80) REVERT: B 449 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7787 (ttm170) REVERT: B 515 LYS cc_start: 0.7391 (mttt) cc_final: 0.7132 (mttt) REVERT: C 20 LYS cc_start: 0.6960 (mppt) cc_final: 0.6629 (mppt) REVERT: C 60 SER cc_start: 0.7362 (p) cc_final: 0.6875 (m) REVERT: C 238 PHE cc_start: 0.4171 (OUTLIER) cc_final: 0.3397 (t80) REVERT: C 305 GLU cc_start: 0.6415 (tp30) cc_final: 0.6192 (mp0) REVERT: C 368 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.5739 (t80) REVERT: C 448 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7287 (tp30) REVERT: C 497 LYS cc_start: 0.8186 (mtpm) cc_final: 0.7962 (mtpp) REVERT: C 518 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6891 (mt-10) REVERT: D 31 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7817 (tp) REVERT: D 92 SER cc_start: 0.7637 (m) cc_final: 0.7270 (p) REVERT: D 246 LYS cc_start: 0.6567 (mttt) cc_final: 0.6222 (mttp) REVERT: D 280 ARG cc_start: 0.7524 (tpp80) cc_final: 0.7191 (ttm110) REVERT: D 360 GLU cc_start: 0.6260 (mt-10) cc_final: 0.5934 (mt-10) REVERT: D 455 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7846 (mtp180) REVERT: E 449 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7697 (ttp-170) outliers start: 36 outliers final: 29 residues processed: 332 average time/residue: 0.5798 time to fit residues: 220.1548 Evaluate side-chains 339 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 531 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [222, 187, 129, 148, 27, 201, 97, 10, 111, 24, 123] chunk 222 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN C 166 GLN C 567 GLN D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.186962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155791 restraints weight = 28874.562| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.31 r_work: 0.3857 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21664 Z= 0.131 Angle : 0.556 10.078 29234 Z= 0.297 Chirality : 0.045 0.316 3297 Planarity : 0.004 0.098 3754 Dihedral : 4.413 32.476 2822 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.32 % Allowed : 17.70 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -0.26 (0.16), residues: 2605 helix: 1.23 (0.19), residues: 872 sheet: 0.15 (0.25), residues: 426 loop : -1.29 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 280 TYR 0.018 0.001 TYR C 404 PHE 0.034 0.002 PHE A 385 TRP 0.016 0.002 TRP E 213 HIS 0.006 0.001 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21664) covalent geometry : angle 0.55578 / 0.30 (29234) hydrogen bonds : bond 0.04259 / 2.76 ( 740) hydrogen bonds : angle 4.36283 / 2.97 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.42 seconds wall clock time: 137 minutes 54.69 seconds (8274.69 seconds total)