Starting phenix.real_space_refine on Wed Mar 4 14:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z38_14473/03_2026/7z38_14473.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 9007 2.51 5 N 2423 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14258 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5173 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 17, 'TRANS': 620} Chain breaks: 1 Chain: "C" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1564 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2299 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.10, per 1000 atoms: 0.22 Number of scatterers: 14258 At special positions: 0 Unit cell: (124.8, 118.976, 152.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 7 15.00 Mg 2 11.99 O 2745 8.00 N 2423 7.00 C 9007 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: 1.24 Conformation dependent library (CDL) restraints added in 343.3 milliseconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 15 sheets defined 52.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.222A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.848A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.624A pdb=" N TYR A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.066A pdb=" N LYS A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.739A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.510A pdb=" N ASN A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 398 through 420 removed outlier: 3.926A pdb=" N LYS A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.538A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.744A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.507A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.159A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.615A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 4.428A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 37 through 61 removed outlier: 4.254A pdb=" N ARG B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.815A pdb=" N ASP B 66 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.098A pdb=" N TYR B 192 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.606A pdb=" N LYS B 284 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 399 through 421 removed outlier: 4.058A pdb=" N VAL B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 3.992A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.899A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.585A pdb=" N VAL B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 515 through 525 removed outlier: 4.115A pdb=" N GLU B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.362A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.574A pdb=" N GLU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 667 Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.988A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 462 removed outlier: 3.778A pdb=" N LEU C 445 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 526 through 543 removed outlier: 3.582A pdb=" N ASP C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 564 removed outlier: 3.935A pdb=" N ILE C 558 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 559 " --> pdb=" O ASP C 555 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 589 removed outlier: 3.507A pdb=" N ARG C 583 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 589 " --> pdb=" O VAL C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.528A pdb=" N SER C 604 " --> pdb=" O PRO C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 74 removed outlier: 4.154A pdb=" N ARG D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 112 removed outlier: 3.776A pdb=" N GLU D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 142 through 155 Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.502A pdb=" N LEU D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 183 through 201 Processing helix chain 'D' and resid 202 through 227 removed outlier: 3.892A pdb=" N GLN D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.743A pdb=" N CYS D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.604A pdb=" N ARG B 168 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.593A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.510A pdb=" N LEU A 217 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 363 removed outlier: 5.491A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 363 removed outlier: 5.491A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 363 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA8, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.850A pdb=" N TYR A 484 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N MET A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 486 " --> pdb=" O MET A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 577 through 580 removed outlier: 6.141A pdb=" N LYS A 577 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 628 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 579 " --> pdb=" O ILE A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.630A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 217 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.856A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AB4, first strand: chain 'B' and resid 511 through 513 removed outlier: 8.917A pdb=" N VAL B 511 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 577 through 579 Processing sheet with id=AB6, first strand: chain 'C' and resid 429 through 430 removed outlier: 3.940A pdb=" N LEU C 429 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 476 " --> pdb=" O LEU C 429 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 1965 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: 2.56 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4683 1.34 - 1.46: 2716 1.46 - 1.58: 6965 1.58 - 1.69: 11 1.69 - 1.81: 126 Bond restraints: 14501 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.42e+00 bond pdb=" N VAL B 592 " pdb=" CA VAL B 592 " ideal model delta sigma weight residual 1.454 1.434 0.020 1.28e-02 6.10e+03 2.46e+00 bond pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.42e+00 bond pdb=" CG1 ILE B 591 " pdb=" CD1 ILE B 591 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CA HIS A 171 " pdb=" C HIS A 171 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.73e+00 ... (remaining 14496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19158 1.91 - 3.83: 287 3.83 - 5.74: 38 5.74 - 7.66: 4 7.66 - 9.57: 2 Bond angle restraints: 19489 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 102.43 9.57 1.40e+00 5.10e-01 4.68e+01 angle pdb=" C GLU D 142 " pdb=" CA GLU D 142 " pdb=" CB GLU D 142 " ideal model delta sigma weight residual 116.63 109.99 6.64 1.16e+00 7.43e-01 3.28e+01 angle pdb=" CA GLU D 142 " pdb=" C GLU D 142 " pdb=" N VAL D 143 " ideal model delta sigma weight residual 119.63 116.66 2.97 8.10e-01 1.52e+00 1.35e+01 angle pdb=" CA LYS A 349 " pdb=" CB LYS A 349 " pdb=" CG LYS A 349 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.55e+00 angle pdb=" C CYS C 424 " pdb=" N GLU C 425 " pdb=" CA GLU C 425 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 19484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7621 17.98 - 35.97: 1006 35.97 - 53.95: 261 53.95 - 71.94: 79 71.94 - 89.92: 39 Dihedral angle restraints: 9006 sinusoidal: 3881 harmonic: 5125 Sorted by residual: dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA A 432 " pdb=" C ALA A 432 " pdb=" N PHE A 433 " pdb=" CA PHE A 433 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 314 " pdb=" CB ASP A 314 " pdb=" CG ASP A 314 " pdb=" OD1 ASP A 314 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 9003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.077: 523 0.077 - 0.115: 127 0.115 - 0.153: 23 0.153 - 0.191: 2 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU C 603 " pdb=" CB LEU C 603 " pdb=" CD1 LEU C 603 " pdb=" CD2 LEU C 603 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2133 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 78 " 0.066 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO A 79 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.021 2.00e-02 2.50e+03 1.76e-02 5.39e+00 pdb=" CG PHE A 32 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 280 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU A 280 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 280 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.011 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 194 2.65 - 3.21: 13194 3.21 - 3.77: 21868 3.77 - 4.34: 30445 4.34 - 4.90: 50781 Nonbonded interactions: 116482 Sorted by model distance: nonbonded pdb=" O ASN A 100 " pdb=" OG1 THR A 104 " model vdw 2.085 3.040 nonbonded pdb=" OH TYR B 520 " pdb=" OE1 GLN B 609 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.138 2.170 nonbonded pdb=" O GLY B 132 " pdb=" OG SER B 135 " model vdw 2.183 3.040 nonbonded pdb=" O GLU B 328 " pdb=" OG SER B 383 " model vdw 2.196 3.040 ... (remaining 116477 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 10 through 690 or resid 801 through 802)) selection = (chain 'B' and (resid 10 through 223 or resid 270 through 802)) } 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=0.00 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.040 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.005 0.127 14501 Z= 0.193 Angle : 0.605 9.574 19489 Z= 0.332 Chirality : 0.042 0.191 2136 Planarity : 0.004 0.094 2486 Dihedral : 18.677 89.919 5676 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.19 % Allowed : 23.11 % Favored : 76.70 % 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: -0.56 (0.21), residues: 1723 helix: 0.82 (0.19), residues: 809 sheet: -1.19 (0.36), residues: 213 loop : -1.50 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 449 TYR 0.025 0.002 TYR A 426 PHE 0.039 0.002 PHE A 32 TRP 0.015 0.002 TRP B 157 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00466 (14501) covalent geometry : angle 0.60499 (19489) hydrogen bonds : bond 0.16708 ( 696) hydrogen bonds : angle 6.53989 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 472 TYR cc_start: 0.7759 (t80) cc_final: 0.7372 (t80) REVERT: D 216 MET cc_start: 0.5061 (mmm) cc_final: 0.4415 (ttt) outliers start: 3 outliers final: 3 residues processed: 177 average time/residue: 0.1256 time to fit residues: 32.2033 Evaluate side-chains 174 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 596 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.202466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148889 restraints weight = 15988.510| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.34 r_work: 0.3576 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14501 Z= 0.160 Angle : 0.544 8.612 19489 Z= 0.291 Chirality : 0.041 0.234 2136 Planarity : 0.004 0.043 2486 Dihedral : 6.708 75.358 1964 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 2.73 % Allowed : 21.71 % Favored : 75.56 % 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: -0.38 (0.21), residues: 1723 helix: 1.02 (0.19), residues: 799 sheet: -1.09 (0.36), residues: 208 loop : -1.44 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.018 0.002 TYR B 134 PHE 0.030 0.002 PHE A 32 TRP 0.018 0.002 TRP B 157 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00376 (14501) covalent geometry : angle 0.54376 (19489) hydrogen bonds : bond 0.04023 ( 696) hydrogen bonds : angle 4.80175 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (t80) REVERT: A 40 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8404 (tt) REVERT: A 406 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: A 554 GLU cc_start: 0.7988 (tp30) cc_final: 0.7026 (mt-10) REVERT: B 85 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 137 TYR cc_start: 0.8770 (m-80) cc_final: 0.8225 (m-80) REVERT: B 472 TYR cc_start: 0.7821 (t80) cc_final: 0.6991 (t80) REVERT: C 462 LYS cc_start: 0.7508 (mmtm) cc_final: 0.7292 (mmtm) REVERT: D 216 MET cc_start: 0.4753 (mmm) cc_final: 0.4366 (ttt) outliers start: 43 outliers final: 20 residues processed: 214 average time/residue: 0.1128 time to fit residues: 35.2455 Evaluate side-chains 203 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.203930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.150071 restraints weight = 16078.286| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.36 r_work: 0.3596 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14501 Z= 0.125 Angle : 0.505 10.063 19489 Z= 0.267 Chirality : 0.040 0.150 2136 Planarity : 0.003 0.044 2486 Dihedral : 6.238 71.822 1957 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 3.43 % Allowed : 21.40 % Favored : 75.17 % 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: -0.21 (0.21), residues: 1723 helix: 1.19 (0.19), residues: 796 sheet: -1.09 (0.36), residues: 203 loop : -1.36 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 36 TYR 0.020 0.001 TYR A 426 PHE 0.026 0.001 PHE A 32 TRP 0.018 0.001 TRP B 157 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00289 (14501) covalent geometry : angle 0.50533 (19489) hydrogen bonds : bond 0.03483 ( 696) hydrogen bonds : angle 4.48399 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (t80) REVERT: A 406 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8153 (mttm) REVERT: A 531 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7012 (ptpp) REVERT: A 554 GLU cc_start: 0.7841 (tp30) cc_final: 0.6993 (mt-10) REVERT: A 663 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 85 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8294 (m) REVERT: B 137 TYR cc_start: 0.8753 (m-80) cc_final: 0.8307 (m-80) REVERT: B 405 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7497 (ttm-80) REVERT: B 472 TYR cc_start: 0.7763 (t80) cc_final: 0.7019 (t80) REVERT: C 462 LYS cc_start: 0.7413 (mmtm) cc_final: 0.7196 (mmtm) REVERT: C 478 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5957 (pp20) REVERT: D 30 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8201 (mtm-85) REVERT: D 216 MET cc_start: 0.4822 (mmm) cc_final: 0.4524 (ttp) outliers start: 54 outliers final: 24 residues processed: 229 average time/residue: 0.1151 time to fit residues: 38.7331 Evaluate side-chains 205 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.202851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148591 restraints weight = 16072.782| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.46 r_work: 0.3591 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14501 Z= 0.159 Angle : 0.539 9.229 19489 Z= 0.281 Chirality : 0.041 0.318 2136 Planarity : 0.003 0.044 2486 Dihedral : 6.259 72.519 1957 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 3.87 % Allowed : 21.14 % Favored : 74.98 % 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: -0.29 (0.21), residues: 1723 helix: 1.10 (0.19), residues: 812 sheet: -1.13 (0.36), residues: 203 loop : -1.41 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 36 TYR 0.022 0.002 TYR A 426 PHE 0.031 0.002 PHE A 32 TRP 0.017 0.001 TRP B 157 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00381 (14501) covalent geometry : angle 0.53941 (19489) hydrogen bonds : bond 0.03477 ( 696) hydrogen bonds : angle 4.43554 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8505 (t80) REVERT: A 151 ASP cc_start: 0.8668 (m-30) cc_final: 0.8440 (m-30) REVERT: A 476 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7593 (ttm) REVERT: A 531 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6972 (ptpp) REVERT: A 663 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 123 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 125 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7260 (mmt) REVERT: B 137 TYR cc_start: 0.8809 (m-80) cc_final: 0.8311 (m-80) REVERT: B 405 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7484 (ttm-80) REVERT: B 472 TYR cc_start: 0.7872 (t80) cc_final: 0.7066 (t80) REVERT: C 462 LYS cc_start: 0.7454 (mmtm) cc_final: 0.7184 (mmtm) REVERT: C 478 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5943 (pp20) REVERT: D 30 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8222 (mtm-85) REVERT: D 216 MET cc_start: 0.4748 (mmm) cc_final: 0.4477 (ttp) outliers start: 61 outliers final: 33 residues processed: 222 average time/residue: 0.1219 time to fit residues: 39.3910 Evaluate side-chains 211 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.204963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150212 restraints weight = 15907.547| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.39 r_work: 0.3579 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14501 Z= 0.131 Angle : 0.517 8.984 19489 Z= 0.271 Chirality : 0.040 0.315 2136 Planarity : 0.003 0.046 2486 Dihedral : 6.159 69.293 1957 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 3.62 % Allowed : 21.59 % Favored : 74.79 % 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: -0.21 (0.21), residues: 1723 helix: 1.19 (0.19), residues: 806 sheet: -1.09 (0.36), residues: 203 loop : -1.39 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 36 TYR 0.015 0.001 TYR B 134 PHE 0.027 0.001 PHE A 32 TRP 0.017 0.001 TRP B 157 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00310 (14501) covalent geometry : angle 0.51653 (19489) hydrogen bonds : bond 0.03260 ( 696) hydrogen bonds : angle 4.32957 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8386 (t80) REVERT: A 151 ASP cc_start: 0.8704 (m-30) cc_final: 0.8469 (m-30) REVERT: A 476 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7525 (ttm) REVERT: A 531 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6991 (ptpp) REVERT: A 554 GLU cc_start: 0.8021 (tp30) cc_final: 0.6947 (mt-10) REVERT: A 663 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 682 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8010 (ptp90) REVERT: B 20 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 123 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7841 (tp) REVERT: B 125 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7164 (mmt) REVERT: B 137 TYR cc_start: 0.8826 (m-80) cc_final: 0.8341 (m-80) REVERT: B 405 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7457 (ttm-80) REVERT: B 472 TYR cc_start: 0.7856 (t80) cc_final: 0.7063 (t80) REVERT: B 553 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5539 (mmm) REVERT: C 462 LYS cc_start: 0.7403 (mmtm) cc_final: 0.7132 (mmtm) REVERT: C 478 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: D 216 MET cc_start: 0.4781 (mmm) cc_final: 0.4483 (ttm) outliers start: 57 outliers final: 40 residues processed: 216 average time/residue: 0.1184 time to fit residues: 37.3221 Evaluate side-chains 216 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 130 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 146 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.200802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146511 restraints weight = 15747.073| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.30 r_work: 0.3537 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14501 Z= 0.224 Angle : 0.596 8.642 19489 Z= 0.311 Chirality : 0.043 0.311 2136 Planarity : 0.004 0.046 2486 Dihedral : 6.418 76.600 1957 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 4.83 % Allowed : 21.21 % Favored : 73.97 % 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: -0.40 (0.20), residues: 1723 helix: 1.07 (0.19), residues: 799 sheet: -1.32 (0.35), residues: 212 loop : -1.46 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 36 TYR 0.022 0.002 TYR B 134 PHE 0.038 0.002 PHE A 32 TRP 0.016 0.002 TRP A 157 HIS 0.005 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00542 (14501) covalent geometry : angle 0.59565 (19489) hydrogen bonds : bond 0.03670 ( 696) hydrogen bonds : angle 4.48435 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 125 MET cc_start: 0.8667 (mmm) cc_final: 0.8378 (mtp) REVERT: A 151 ASP cc_start: 0.8710 (m-30) cc_final: 0.8453 (m-30) REVERT: A 326 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7018 (tm130) REVERT: A 476 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7481 (ttm) REVERT: A 531 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7042 (ptpp) REVERT: A 554 GLU cc_start: 0.8077 (tp30) cc_final: 0.6996 (mt-10) REVERT: A 663 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 682 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8004 (ptp90) REVERT: B 20 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 123 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7864 (tp) REVERT: B 125 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7487 (mmt) REVERT: B 308 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8299 (tp) REVERT: B 472 TYR cc_start: 0.8031 (t80) cc_final: 0.7140 (t80) REVERT: B 524 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: B 553 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5459 (mmm) REVERT: C 430 TYR cc_start: 0.5789 (m-80) cc_final: 0.5122 (m-80) REVERT: C 462 LYS cc_start: 0.7436 (mmtm) cc_final: 0.7158 (mmtm) REVERT: C 478 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5857 (pp20) REVERT: C 512 MET cc_start: 0.2356 (tpt) cc_final: 0.1908 (mmt) REVERT: D 216 MET cc_start: 0.4820 (mmm) cc_final: 0.4493 (ttp) outliers start: 76 outliers final: 47 residues processed: 229 average time/residue: 0.1145 time to fit residues: 38.5597 Evaluate side-chains 229 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.203889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153175 restraints weight = 15836.991| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.75 r_work: 0.3552 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14501 Z= 0.142 Angle : 0.531 8.569 19489 Z= 0.279 Chirality : 0.041 0.312 2136 Planarity : 0.003 0.046 2486 Dihedral : 6.230 71.672 1957 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 4.32 % Allowed : 21.84 % Favored : 73.84 % 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: -0.25 (0.20), residues: 1723 helix: 1.18 (0.19), residues: 801 sheet: -1.25 (0.36), residues: 203 loop : -1.37 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 36 TYR 0.029 0.002 TYR A 426 PHE 0.035 0.002 PHE A 32 TRP 0.017 0.001 TRP B 157 HIS 0.005 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00336 (14501) covalent geometry : angle 0.53143 (19489) hydrogen bonds : bond 0.03321 ( 696) hydrogen bonds : angle 4.33085 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8689 (mmm) cc_final: 0.8203 (mtp) REVERT: A 151 ASP cc_start: 0.8704 (m-30) cc_final: 0.8466 (m-30) REVERT: A 326 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7213 (tm130) REVERT: A 476 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7462 (ttm) REVERT: A 531 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6981 (ptpp) REVERT: A 554 GLU cc_start: 0.8024 (tp30) cc_final: 0.6967 (mt-10) REVERT: A 617 MET cc_start: 0.7010 (tpp) cc_final: 0.6539 (mmm) REVERT: A 663 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 682 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7924 (ptp90) REVERT: B 20 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 123 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7830 (tp) REVERT: B 125 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7134 (mmt) REVERT: B 137 TYR cc_start: 0.8914 (m-80) cc_final: 0.8299 (m-80) REVERT: B 472 TYR cc_start: 0.7956 (t80) cc_final: 0.7111 (t80) REVERT: B 553 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5457 (mmm) REVERT: C 462 LYS cc_start: 0.7371 (mmtm) cc_final: 0.7098 (mmtm) REVERT: C 467 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.2297 (mtp85) REVERT: C 478 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5806 (pp20) REVERT: C 512 MET cc_start: 0.2318 (tpt) cc_final: 0.1895 (mmt) REVERT: D 216 MET cc_start: 0.4810 (mmm) cc_final: 0.4552 (ttp) outliers start: 68 outliers final: 45 residues processed: 219 average time/residue: 0.1201 time to fit residues: 38.3437 Evaluate side-chains 222 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 561 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 106 optimal weight: 0.0770 chunk 125 optimal weight: 0.7980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.206922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153457 restraints weight = 15882.743| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.95 r_work: 0.3602 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14501 Z= 0.099 Angle : 0.490 8.522 19489 Z= 0.259 Chirality : 0.039 0.149 2136 Planarity : 0.003 0.048 2486 Dihedral : 5.941 62.726 1957 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 3.05 % Allowed : 22.86 % Favored : 74.10 % 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: -0.07 (0.21), residues: 1723 helix: 1.30 (0.19), residues: 813 sheet: -1.10 (0.36), residues: 203 loop : -1.31 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 449 TYR 0.023 0.001 TYR A 426 PHE 0.024 0.001 PHE A 32 TRP 0.018 0.001 TRP B 157 HIS 0.004 0.000 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00215 (14501) covalent geometry : angle 0.49022 (19489) hydrogen bonds : bond 0.02998 ( 696) hydrogen bonds : angle 4.12648 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 531 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.6957 (ptpp) REVERT: A 554 GLU cc_start: 0.7847 (tp30) cc_final: 0.6972 (mt-10) REVERT: A 617 MET cc_start: 0.7095 (tpp) cc_final: 0.6656 (mmm) REVERT: A 663 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 682 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7819 (ptp90) REVERT: B 123 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7902 (tp) REVERT: B 137 TYR cc_start: 0.8738 (m-80) cc_final: 0.8258 (m-80) REVERT: B 405 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7273 (ttm-80) REVERT: B 472 TYR cc_start: 0.7624 (t80) cc_final: 0.6934 (t80) REVERT: C 462 LYS cc_start: 0.7280 (mmtm) cc_final: 0.6983 (mmtm) REVERT: C 478 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5890 (pp20) REVERT: C 512 MET cc_start: 0.1951 (tpt) cc_final: 0.1662 (mmt) REVERT: D 216 MET cc_start: 0.4769 (mmm) cc_final: 0.4552 (ttp) outliers start: 48 outliers final: 32 residues processed: 223 average time/residue: 0.1242 time to fit residues: 39.7964 Evaluate side-chains 211 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 561 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 147 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 154 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.205487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151112 restraints weight = 16002.486| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.46 r_work: 0.3591 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14501 Z= 0.119 Angle : 0.521 8.829 19489 Z= 0.271 Chirality : 0.040 0.289 2136 Planarity : 0.003 0.045 2486 Dihedral : 5.971 63.933 1957 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.11 % Favored : 94.78 % Rotamer: Outliers : 2.98 % Allowed : 22.98 % Favored : 74.03 % 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: -0.07 (0.21), residues: 1723 helix: 1.30 (0.19), residues: 813 sheet: -1.11 (0.36), residues: 203 loop : -1.30 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 449 TYR 0.022 0.001 TYR A 426 PHE 0.026 0.001 PHE A 32 TRP 0.016 0.001 TRP B 157 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00278 (14501) covalent geometry : angle 0.52142 (19489) hydrogen bonds : bond 0.03076 ( 696) hydrogen bonds : angle 4.15644 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 476 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7498 (ttm) REVERT: A 531 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: A 554 GLU cc_start: 0.7842 (tp30) cc_final: 0.6941 (mt-10) REVERT: A 617 MET cc_start: 0.7092 (tpp) cc_final: 0.6684 (mmm) REVERT: A 663 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 682 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7972 (ptp90) REVERT: B 20 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: B 123 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 137 TYR cc_start: 0.8738 (m-80) cc_final: 0.8234 (m-80) REVERT: B 405 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.7282 (ttm-80) REVERT: B 472 TYR cc_start: 0.7752 (t80) cc_final: 0.6981 (t80) REVERT: C 462 LYS cc_start: 0.7309 (mmtm) cc_final: 0.7010 (mmtm) REVERT: C 478 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5907 (pp20) REVERT: C 512 MET cc_start: 0.1989 (tpt) cc_final: 0.1719 (mmt) REVERT: D 216 MET cc_start: 0.4827 (mmm) cc_final: 0.4597 (ttp) outliers start: 47 outliers final: 33 residues processed: 206 average time/residue: 0.1196 time to fit residues: 35.9651 Evaluate side-chains 211 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 159 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 chunk 102 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.205236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149991 restraints weight = 15920.423| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.46 r_work: 0.3580 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14501 Z= 0.133 Angle : 0.531 8.633 19489 Z= 0.276 Chirality : 0.040 0.155 2136 Planarity : 0.003 0.049 2486 Dihedral : 5.976 64.470 1957 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 2.79 % Allowed : 23.17 % Favored : 74.03 % 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: -0.12 (0.20), residues: 1723 helix: 1.27 (0.19), residues: 814 sheet: -1.17 (0.35), residues: 208 loop : -1.34 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 449 TYR 0.021 0.002 TYR A 426 PHE 0.029 0.002 PHE A 32 TRP 0.016 0.001 TRP B 157 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00316 (14501) covalent geometry : angle 0.53058 (19489) hydrogen bonds : bond 0.03159 ( 696) hydrogen bonds : angle 4.16020 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: A 531 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6985 (ptpp) REVERT: A 554 GLU cc_start: 0.8030 (tp30) cc_final: 0.6962 (mt-10) REVERT: A 617 MET cc_start: 0.7063 (tpp) cc_final: 0.6591 (mmp) REVERT: A 663 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 682 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: B 20 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: B 123 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 137 TYR cc_start: 0.8876 (m-80) cc_final: 0.8319 (m-80) REVERT: B 405 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7466 (ttm-80) REVERT: B 472 TYR cc_start: 0.7917 (t80) cc_final: 0.7052 (t80) REVERT: C 462 LYS cc_start: 0.7350 (mmtm) cc_final: 0.7049 (mmtm) REVERT: C 478 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5850 (pp20) REVERT: C 512 MET cc_start: 0.2192 (tpt) cc_final: 0.1841 (mmt) REVERT: D 99 GLU cc_start: 0.3552 (mm-30) cc_final: 0.2788 (pm20) REVERT: D 216 MET cc_start: 0.4786 (mmm) cc_final: 0.4476 (ttp) outliers start: 44 outliers final: 32 residues processed: 197 average time/residue: 0.1186 time to fit residues: 33.8845 Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain D residue 9 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 170 optimal weight: 5.9990 chunk 11 optimal weight: 0.0000 chunk 137 optimal weight: 0.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.206448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.151496 restraints weight = 15982.531| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.47 r_work: 0.3592 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14501 Z= 0.120 Angle : 0.524 9.751 19489 Z= 0.272 Chirality : 0.040 0.294 2136 Planarity : 0.003 0.047 2486 Dihedral : 5.921 63.537 1957 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 2.92 % Allowed : 23.17 % Favored : 73.90 % 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: -0.07 (0.21), residues: 1723 helix: 1.31 (0.19), residues: 814 sheet: -1.14 (0.35), residues: 208 loop : -1.32 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 449 TYR 0.021 0.001 TYR A 426 PHE 0.026 0.001 PHE A 32 TRP 0.017 0.001 TRP B 157 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00281 (14501) covalent geometry : angle 0.52373 (19489) hydrogen bonds : bond 0.03083 ( 696) hydrogen bonds : angle 4.15174 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4287.38 seconds wall clock time: 73 minutes 53.70 seconds (4433.70 seconds total)