Starting phenix.real_space_refine on Thu Feb 5 20:37:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qco_53017/02_2026/9qco_53017.map" } resolution = 2.76 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= -0.001 sd= 1.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 12701 2.51 5 N 3235 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19569 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7457 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 299} Link IDs: {'PTRANS': 33, 'TRANS': 1000} Chain breaks: 8 Unresolved non-hydrogen bonds: 1011 Unresolved non-hydrogen angles: 1256 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASN:plan1': 44, 'ASP:plan': 46, 'ARG:plan': 8, 'GLU:plan': 54, 'GLN:plan1': 19, 'TYR:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 640 Chain: "B" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4081 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 537} Chain breaks: 9 Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 549 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 25, 'GLU:plan': 24, 'GLN:plan1': 6, 'HIS:plan': 1, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 279 Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 3954 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 22, 'TRANS': 532} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 686 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 31, 'GLU:plan': 29, 'GLN:plan1': 13, 'ARG:plan': 7, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 357 Chain: "D" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4077 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 545} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 524 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 33, 'GLU:plan': 26, 'GLN:plan1': 10, 'ARG:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 320 Time building chain proxies: 4.63, per 1000 atoms: 0.24 Number of scatterers: 19569 At special positions: 0 Unit cell: (157.32, 150.696, 168.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3597 8.00 N 3235 7.00 C 12701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 754 " distance=2.03 Simple disulfide: pdb=" SG CYS A 927 " - pdb=" SG CYS A 945 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5174 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 29 sheets defined 20.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.447A pdb=" N THR A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.586A pdb=" N LEU A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.639A pdb=" N GLU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.728A pdb=" N GLU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.992A pdb=" N GLY A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 4.011A pdb=" N LYS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 removed outlier: 4.233A pdb=" N SER A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 4.097A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.749A pdb=" N ILE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 3.937A pdb=" N PHE A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.033A pdb=" N PHE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.891A pdb=" N ASN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.922A pdb=" N GLN A 393 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 395 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.658A pdb=" N GLN A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 554 through 574 removed outlier: 4.677A pdb=" N PHE A 571 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.728A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.722A pdb=" N GLU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 676 Processing helix chain 'A' and resid 676 through 711 removed outlier: 3.530A pdb=" N TYR A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 760 removed outlier: 3.684A pdb=" N ILE A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 4.058A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 4.109A pdb=" N GLN A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.693A pdb=" N PHE A 808 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 820 removed outlier: 3.597A pdb=" N ILE A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 1024 through 1037 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.792A pdb=" N VAL B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.099A pdb=" N GLN B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.588A pdb=" N SER B 289 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.524A pdb=" N ARG B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.205A pdb=" N TYR C 168 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.563A pdb=" N LEU C 507 " --> pdb=" O LEU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.111A pdb=" N TYR D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 422 through 426 Processing helix chain 'D' and resid 503 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 7.034A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 215 removed outlier: 4.506A pdb=" N SER A 387 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 248 removed outlier: 5.708A pdb=" N LEU A 260 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 247 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 405 removed outlier: 5.987A pdb=" N ASN A 404 " --> pdb=" O THR A 495 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 581 removed outlier: 3.616A pdb=" N GLY A 584 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 835 through 842 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 849 through 852 current: chain 'A' and resid 875 through 878 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 875 through 878 current: chain 'A' and resid 960 through 970 removed outlier: 5.595A pdb=" N LEU A 976 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 987 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 978 " --> pdb=" O ILE A 985 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 859 through 862 removed outlier: 7.668A pdb=" N THR A1001 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A 923 " --> pdb=" O THR A1001 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 938 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 28 through 33 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 33 current: chain 'B' and resid 138 through 157 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 138 through 157 current: chain 'B' and resid 355 through 356 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'B' and resid 57 through 64 removed outlier: 3.906A pdb=" N PHE B 293 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 103 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 293 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 217 through 227 current: chain 'B' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 325 through 335 current: chain 'B' and resid 454 through 455 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 233 through 239 removed outlier: 3.652A pdb=" N CYS B 306 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 381 through 384 removed outlier: 6.537A pdb=" N ASN B 381 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU B 409 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN B 383 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 459 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 392 through 396 removed outlier: 6.175A pdb=" N SER B 511 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU B 540 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN B 513 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N THR B 542 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 568 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 442 through 443 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 442 through 443 current: chain 'D' and resid 138 through 147 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 138 through 147 current: chain 'D' and resid 354 through 356 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 524 through 529 Processing sheet with id=AC2, first strand: chain 'C' and resid 28 through 39 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 39 current: chain 'C' and resid 138 through 157 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 216 through 227 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 216 through 227 current: chain 'C' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 325 through 335 current: chain 'C' and resid 406 through 410 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 406 through 410 current: chain 'C' and resid 454 through 459 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 233 through 239 Processing sheet with id=AC5, first strand: chain 'C' and resid 392 through 396 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 392 through 396 current: chain 'C' and resid 468 through 474 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 468 through 474 current: chain 'C' and resid 536 through 541 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 536 through 541 current: chain 'C' and resid 581 through 585 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 525 through 529 Processing sheet with id=AC7, first strand: chain 'D' and resid 49 through 53 removed outlier: 4.030A pdb=" N ASN D 116 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 215 through 227 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 227 current: chain 'D' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 325 through 335 current: chain 'D' and resid 406 through 410 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 406 through 410 current: chain 'D' and resid 454 through 460 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 233 through 239 Processing sheet with id=AD1, first strand: chain 'D' and resid 392 through 396 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 392 through 396 current: chain 'D' and resid 468 through 474 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 468 through 474 current: chain 'D' and resid 537 through 541 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 537 through 541 current: chain 'D' and resid 581 through 585 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 525 through 529 613 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4864 1.33 - 1.45: 4028 1.45 - 1.57: 11038 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 19982 Sorted by residual: bond pdb=" N PRO B 531 " pdb=" CD PRO B 531 " ideal model delta sigma weight residual 1.473 1.356 0.117 1.40e-02 5.10e+03 6.93e+01 bond pdb=" N PRO A 551 " pdb=" CD PRO A 551 " ideal model delta sigma weight residual 1.473 1.370 0.103 1.40e-02 5.10e+03 5.44e+01 bond pdb=" CA TYR A 569 " pdb=" C TYR A 569 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.35e-02 5.49e+03 3.41e+01 bond pdb=" CA TYR A 558 " pdb=" C TYR A 558 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.56e+01 bond pdb=" CA SER A 570 " pdb=" CB SER A 570 " ideal model delta sigma weight residual 1.530 1.464 0.065 1.63e-02 3.76e+03 1.60e+01 ... (remaining 19977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26907 2.28 - 4.56: 351 4.56 - 6.84: 69 6.84 - 9.12: 20 9.12 - 11.40: 6 Bond angle restraints: 27353 Sorted by residual: angle pdb=" N ASN A 568 " pdb=" CA ASN A 568 " pdb=" C ASN A 568 " ideal model delta sigma weight residual 114.04 103.73 10.31 1.24e+00 6.50e-01 6.91e+01 angle pdb=" N ILE D 514 " pdb=" CA ILE D 514 " pdb=" CB ILE D 514 " ideal model delta sigma weight residual 111.66 103.16 8.50 1.14e+00 7.69e-01 5.56e+01 angle pdb=" C GLU A 695 " pdb=" CA GLU A 695 " pdb=" CB GLU A 695 " ideal model delta sigma weight residual 110.86 99.46 11.40 1.65e+00 3.67e-01 4.78e+01 angle pdb=" N GLU C 380 " pdb=" CA GLU C 380 " pdb=" C GLU C 380 " ideal model delta sigma weight residual 110.50 120.22 -9.72 1.41e+00 5.03e-01 4.75e+01 angle pdb=" N PRO C 378 " pdb=" CA PRO C 378 " pdb=" C PRO C 378 " ideal model delta sigma weight residual 113.86 105.92 7.94 1.25e+00 6.40e-01 4.03e+01 ... (remaining 27348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10533 17.86 - 35.71: 858 35.71 - 53.57: 188 53.57 - 71.43: 40 71.43 - 89.29: 16 Dihedral angle restraints: 11635 sinusoidal: 3599 harmonic: 8036 Sorted by residual: dihedral pdb=" CD ARG C 499 " pdb=" NE ARG C 499 " pdb=" CZ ARG C 499 " pdb=" NH1 ARG C 499 " ideal model delta sinusoidal sigma weight residual 0.00 88.54 -88.54 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA TYR A 368 " pdb=" C TYR A 368 " pdb=" N PRO A 369 " pdb=" CA PRO A 369 " ideal model delta harmonic sigma weight residual 180.00 145.94 34.06 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CB CYS A 583 " pdb=" SG CYS A 583 " pdb=" SG CYS A 754 " pdb=" CB CYS A 754 " ideal model delta sinusoidal sigma weight residual 93.00 149.75 -56.75 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 11632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2767 0.069 - 0.139: 427 0.139 - 0.208: 29 0.208 - 0.278: 9 0.278 - 0.347: 6 Chirality restraints: 3238 Sorted by residual: chirality pdb=" CA VAL D 512 " pdb=" N VAL D 512 " pdb=" C VAL D 512 " pdb=" CB VAL D 512 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA GLU A 695 " pdb=" N GLU A 695 " pdb=" C GLU A 695 " pdb=" CB GLU A 695 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA ILE D 514 " pdb=" N ILE D 514 " pdb=" C ILE D 514 " pdb=" CB ILE D 514 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 3235 not shown) Planarity restraints: 3506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 499 " -1.129 9.50e-02 1.11e+02 5.06e-01 1.54e+02 pdb=" NE ARG C 499 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 499 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 499 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 499 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 388 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA C 388 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA C 388 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE C 389 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 279 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A 280 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " -0.036 5.00e-02 4.00e+02 ... (remaining 3503 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 4 2.15 - 2.84: 6844 2.84 - 3.53: 25506 3.53 - 4.21: 45927 4.21 - 4.90: 80422 Nonbonded interactions: 158703 Sorted by model distance: nonbonded pdb=" O ILE A 178 " pdb=" OE1 GLN A 204 " model vdw 1.467 3.040 nonbonded pdb=" O ASN B 588 " pdb=" OG SER B 592 " model vdw 1.913 3.040 nonbonded pdb=" OG SER B 78 " pdb=" OE2 GLU B 140 " model vdw 2.095 3.040 nonbonded pdb=" OD2 ASP A 349 " pdb=" OG SER A 822 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR A 278 " pdb=" O PRO A 280 " model vdw 2.183 3.040 ... (remaining 158698 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 'B' and (resid 22 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 51 or (resid 52 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and ( \ name N or name CA or name C or name O or name CB )) or resid 57 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 80 or (resid 81 through 82 and (name N or name CA or name C or name O or na \ me CB )) or resid 83 through 99 or (resid 100 and (name N or name CA or name C o \ r name O or name CB )) or resid 101 through 105 or (resid 106 and (name N or nam \ e CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 163 \ or (resid 164 through 166 and (name N or name CA or name C or name O or name CB \ )) or resid 167 through 176 or (resid 177 through 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 252 or (resi \ d 253 through 255 and (name N or name CA or name C or name O or name CB )) or re \ sid 256 through 260 or (resid 261 and (name N or name CA or name C or name O or \ name CB )) or resid 262 through 263 or (resid 264 through 267 and (name N or nam \ e CA or name C or name O or name CB )) or resid 268 through 269 or (resid 270 th \ rough 271 and (name N or name CA or name C or name O or name CB )) or resid 272 \ through 277 or (resid 278 through 280 and (name N or name CA or name C or name O \ or name CB )) or resid 281 through 283 or (resid 284 through 285 and (name N or \ name CA or name C or name O or name CB )) or resid 286 or (resid 287 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 289 or (resi \ d 290 and (name N or name CA or name C or name O or name CB )) or resid 291 thro \ ugh 303 or (resid 304 through 305 and (name N or name CA or name C or name O or \ name CB )) or resid 306 through 340 or (resid 341 and (name N or name CA or name \ C or name O or name CB )) or resid 342 through 343 or (resid 344 through 354 an \ d (name N or name CA or name C or name O or name CB )) or resid 355 through 376 \ or (resid 377 and (name N or name CA or name C or name O or name CB )) or resid \ 378 through 381 or (resid 382 through 384 and (name N or name CA or name C or na \ me O or name CB )) or resid 385 through 389 or (resid 390 through 392 and (name \ N or name CA or name C or name O or name CB )) or resid 393 or (resid 394 and (n \ ame N or name CA or name C or name O or name CB )) or resid 395 through 413 or ( \ resid 414 and (name N or name CA or name C or name O or name CB )) or resid 415 \ through 420 or (resid 421 through 424 and (name N or name CA or name C or name O \ or name CB )) or resid 425 or (resid 426 and (name N or name CA or name C or na \ me O or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C o \ r name O or name CB )) or resid 429 through 432 or (resid 433 through 434 and (n \ ame N or name CA or name C or name O or name CB )) or resid 435 through 443 or ( \ resid 444 and (name N or name CA or name C or name O or name CB )) or resid 445 \ through 467 or (resid 468 and (name N or name CA or name C or name O or name CB \ )) or resid 469 through 483 or (resid 484 and (name N or name CA or name C or na \ me O or name CB )) or resid 485 through 493 or (resid 494 and (name N or name CA \ or name C or name O or name CB )) or resid 495 through 507 or (resid 508 and (n \ ame N or name CA or name C or name O or name CB )) or resid 509 or (resid 510 th \ rough 518 and (name N or name CA or name C or name O or name CB )) or (resid 524 \ and (name N or name CA or name C or name O or name CB )) or resid 525 through 5 \ 27 or (resid 528 through 529 and (name N or name CA or name C or name O or name \ CB )) or resid 530 through 531 or (resid 532 and (name N or name CA or name C or \ name O or name CB )) or resid 533 through 541 or (resid 542 through 543 and (na \ me N or name CA or name C or name O or name CB )) or resid 556 through 558 or (r \ esid 559 and (name N or name CA or name C or name O or name CB )) or resid 560 t \ hrough 566 or (resid 567 through 568 and (name N or name CA or name C or name O \ or name CB )) or resid 569 through 570 or (resid 571 through 600 and (name N or \ name CA or name C or name O or name CB )) or (resid 603 through 604 and (name N \ or name CA or name C or name O or name CB )) or resid 605 or (resid 606 through \ 607 and (name N or name CA or name C or name O or name CB )) or resid 608 throug \ h 623)) selection = (chain 'C' and (resid 22 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 51 or (resid 52 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and ( \ name N or name CA or name C or name O or name CB )) or resid 57 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ (resid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 \ through 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) \ or resid 86 through 93 or (resid 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 through 108 or (resid 109 and (name N or name CA or na \ me C or name O or name CB )) or resid 110 through 133 or (resid 134 through 138 \ and (name N or name CA or name C or name O or name CB )) or resid 139 through 17 \ 3 or (resid 174 and (name N or name CA or name C or name O or name CB )) or resi \ d 175 or (resid 176 through 179 and (name N or name CA or name C or name O or na \ me CB )) or resid 180 through 185 or (resid 186 through 208 and (name N or name \ CA or name C or name O or name CB )) or resid 209 through 229 or (resid 230 and \ (name N or name CA or name C or name O or name CB )) or resid 231 through 253 or \ (resid 254 through 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 through 284 or (resid 285 and (name N or name CA or name C or name \ O or name CB )) or resid 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 289 or (resid 290 and (name N or name \ CA or name C or name O or name CB )) or resid 291 through 303 or (resid 304 thro \ ugh 305 and (name N or name CA or name C or name O or name CB )) or resid 306 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 345 or (resid 352 through 354 and (name N or name CA or na \ me C or name O or name CB )) or resid 355 through 369 or (resid 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or \ resid 418 through 450 or (resid 451 and (name N or name CA or name C or name O o \ r name CB )) or resid 452 through 505 or (resid 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 or (resid 508 and (name N or name CA o \ r name C or name O or name CB )) or resid 509 or (resid 510 through 524 and (nam \ e N or name CA or name C or name O or name CB )) or resid 525 through 527 or (re \ sid 528 through 529 and (name N or name CA or name C or name O or name CB )) or \ resid 530 through 531 or (resid 532 and (name N or name CA or name C or name O o \ r name CB )) or resid 533 through 542 or (resid 555 through 556 and (name N or n \ ame CA or name C or name O or name CB )) or resid 557 through 558 or (resid 559 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 56 \ 7 or (resid 568 and (name N or name CA or name C or name O or name CB )) or resi \ d 569 through 582 or (resid 583 through 604 and (name N or name CA or name C or \ name O or name CB )) or resid 605 or (resid 606 through 607 and (name N or name \ CA or name C or name O or name CB )) or resid 608 or (resid 609 through 610 and \ (name N or name CA or name C or name O or name CB )) or resid 611 through 623)) selection = (chain 'D' and ((resid 22 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 66 or resid 70 through 84 or (resid 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 93 or (res \ id 94 and (name N or name CA or name C or name O or name CB )) or resid 95 throu \ gh 98 or (resid 99 through 100 and (name N or name CA or name C or name O or nam \ e CB )) or resid 101 through 133 or (resid 134 through 138 and (name N or name C \ A or name C or name O or name CB )) or resid 139 through 173 or (resid 174 and ( \ name N or name CA or name C or name O or name CB )) or resid 175 or (resid 176 t \ hrough 179 and (name N or name CA or name C or name O or name CB )) or resid 180 \ through 181 or (resid 182 and (name N or name CA or name C or name O or name CB \ )) or resid 183 or (resid 184 through 187 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 208 and (name N or name CA or name C or name O or \ name CB )) or resid 209 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 252 or (resid 253 through 255 an \ d (name N or name CA or name C or name O or name CB )) or resid 256 or (resid 25 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 258 through \ 260 or (resid 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 through 269 or (resid 270 through 271 and (name N or name CA or name C o \ r name O or name CB )) or resid 272 through 273 or (resid 274 through 275 and (n \ ame N or name CA or name C or name O or name CB )) or resid 276 through 278 or ( \ resid 279 through 280 and (name N or name CA or name C or name O or name CB )) o \ r resid 281 through 296 or (resid 297 through 299 and (name N or name CA or name \ C or name O or name CB )) or resid 300 through 304 or (resid 305 and (name N or \ name CA or name C or name O or name CB )) or resid 306 through 322 or (resid 32 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 324 or (resi \ d 325 and (name N or name CA or name C or name O or name CB )) or resid 326 thro \ ugh 342 or (resid 343 through 345 and (name N or name CA or name C or name O or \ name CB )) or (resid 352 through 354 and (name N or name CA or name C or name O \ or name CB )) or resid 355 through 369 or (resid 370 and (name N or name CA or n \ ame C or name O or name CB )) or resid 371 through 376 or (resid 377 and (name N \ or name CA or name C or name O or name CB )) or resid 378 through 381 or (resid \ 382 through 384 and (name N or name CA or name C or name O or name CB )) or res \ id 385 through 389 or (resid 390 through 392 and (name N or name CA or name C or \ name O or name CB )) or resid 393 through 398 or (resid 402 through 404 and (na \ me N or name CA or name C or name O or name CB )) or resid 405 through 416 or (r \ esid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 t \ hrough 420 or (resid 421 through 424 and (name N or name CA or name C or name O \ or name CB )) or resid 425 through 427 or (resid 428 and (name N or name CA or n \ ame C or name O or name CB )) or resid 429 through 438 or (resid 439 and (name N \ or name CA or name C or name O or name CB )) or resid 440 through 449 or (resid \ 450 through 451 and (name N or name CA or name C or name O or name CB )) or res \ id 452 through 461 or (resid 462 through 463 and (name N or name CA or name C or \ name O or name CB )) or resid 464 through 477 or (resid 478 and (name N or name \ CA or name C or name O or name CB )) or resid 479 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 493 o \ r (resid 494 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 95 through 511 or (resid 512 through 518 and (name N or name CA or name C or nam \ e O or name CB )) or resid 524 through 528 or (resid 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 543 or (resid 556 and (na \ me N or name CA or name C or name O or name CB )) or resid 557 through 563 or (r \ esid 565 and (name N or name CA or name C or name O or name CB )) or resid 566 t \ hrough 573 or (resid 578 through 604 and (name N or name CA or name C or name O \ or name CB )) or resid 605 through 608 or (resid 609 through 610 and (name N or \ name CA or name C or name O or name CB )) or resid 611 through 612 or (resid 613 \ and (name N or name CA or name C or name O or name CB )) or resid 614 through 6 \ 19 or (resid 620 and (name N or name CA or name C or name O or name CB )) or res \ id 621 through 623)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.690 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 19984 Z= 0.206 Angle : 0.672 11.404 27357 Z= 0.422 Chirality : 0.052 0.347 3238 Planarity : 0.009 0.506 3506 Dihedral : 14.561 89.287 6455 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.92 % Rotamer: Outliers : 1.60 % Allowed : 22.35 % Favored : 76.05 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.64 (0.17), residues: 2640 helix: 0.46 (0.25), residues: 479 sheet: 0.16 (0.17), residues: 871 loop : -1.16 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 499 TYR 0.021 0.001 TYR A 569 PHE 0.017 0.001 PHE B 286 TRP 0.018 0.001 TRP A 561 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00337 (19982) covalent geometry : angle 0.67208 (27353) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.60409 ( 4) hydrogen bonds : bond 0.15773 ( 613) hydrogen bonds : angle 6.77899 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.810 Fit side-chains REVERT: A 187 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (tptm) REVERT: A 414 MET cc_start: 0.7881 (mtt) cc_final: 0.7435 (mtm) REVERT: A 540 MET cc_start: 0.7959 (mtm) cc_final: 0.7713 (mtp) REVERT: B 106 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: B 140 GLU cc_start: 0.7947 (tt0) cc_final: 0.7019 (tp30) REVERT: C 442 PHE cc_start: 0.7154 (t80) cc_final: 0.6741 (t80) REVERT: C 538 SER cc_start: 0.9248 (m) cc_final: 0.8972 (p) REVERT: C 583 ILE cc_start: 0.8105 (mt) cc_final: 0.7825 (mp) REVERT: D 609 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7043 (tm-30) outliers start: 28 outliers final: 16 residues processed: 128 average time/residue: 0.4209 time to fit residues: 65.1006 Evaluate side-chains 116 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 568 ASN B 582 ASN C 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076998 restraints weight = 43228.887| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.77 r_work: 0.3077 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19984 Z= 0.125 Angle : 0.486 7.140 27357 Z= 0.264 Chirality : 0.045 0.157 3238 Planarity : 0.003 0.057 3506 Dihedral : 4.827 50.273 2949 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 2.87 % Allowed : 20.34 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.45 (0.17), residues: 2640 helix: 0.97 (0.25), residues: 486 sheet: 0.18 (0.17), residues: 881 loop : -1.14 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.014 0.001 TYR C 310 PHE 0.020 0.001 PHE B 569 TRP 0.009 0.001 TRP A 906 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00282 (19982) covalent geometry : angle 0.48626 (27353) SS BOND : bond 0.00122 ( 2) SS BOND : angle 1.28930 ( 4) hydrogen bonds : bond 0.03583 ( 613) hydrogen bonds : angle 5.03385 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.851 Fit side-chains REVERT: A 414 MET cc_start: 0.7846 (mtt) cc_final: 0.7322 (mtm) REVERT: A 540 MET cc_start: 0.7717 (mtm) cc_final: 0.7468 (mtp) REVERT: A 960 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.5646 (tptp) REVERT: B 88 ILE cc_start: 0.9210 (mm) cc_final: 0.8930 (mp) REVERT: B 140 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6798 (tp30) REVERT: B 251 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8346 (mtt180) REVERT: B 555 ILE cc_start: 0.9179 (mm) cc_final: 0.8955 (pp) REVERT: C 389 ILE cc_start: 0.8958 (mm) cc_final: 0.8498 (mm) REVERT: C 442 PHE cc_start: 0.7332 (t80) cc_final: 0.6948 (t80) REVERT: C 538 SER cc_start: 0.9269 (m) cc_final: 0.8973 (p) REVERT: C 583 ILE cc_start: 0.8070 (mt) cc_final: 0.7820 (mp) REVERT: D 609 GLU cc_start: 0.7624 (tm-30) cc_final: 0.6854 (tm-30) outliers start: 50 outliers final: 18 residues processed: 156 average time/residue: 0.4140 time to fit residues: 78.1997 Evaluate side-chains 118 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 94 optimal weight: 0.0170 chunk 233 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 529 GLN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.077944 restraints weight = 43348.580| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.79 r_work: 0.3096 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19984 Z= 0.095 Angle : 0.457 7.262 27357 Z= 0.247 Chirality : 0.045 0.155 3238 Planarity : 0.003 0.058 3506 Dihedral : 4.257 49.731 2925 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 2.92 % Allowed : 21.38 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.23 (0.17), residues: 2640 helix: 1.41 (0.25), residues: 484 sheet: 0.24 (0.17), residues: 876 loop : -1.05 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 127 TYR 0.014 0.001 TYR C 310 PHE 0.019 0.001 PHE A 810 TRP 0.006 0.001 TRP A 906 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00210 (19982) covalent geometry : angle 0.45689 (27353) SS BOND : bond 0.00102 ( 2) SS BOND : angle 1.12244 ( 4) hydrogen bonds : bond 0.03129 ( 613) hydrogen bonds : angle 4.73289 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.849 Fit side-chains REVERT: A 179 VAL cc_start: 0.8797 (p) cc_final: 0.8535 (m) REVERT: A 186 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8871 (t80) REVERT: A 382 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 414 MET cc_start: 0.7857 (mtt) cc_final: 0.7338 (mtm) REVERT: A 540 MET cc_start: 0.7733 (mtm) cc_final: 0.7488 (mtp) REVERT: A 1011 ILE cc_start: 0.9058 (pt) cc_final: 0.8733 (pp) REVERT: B 88 ILE cc_start: 0.9235 (mm) cc_final: 0.8950 (mp) REVERT: B 251 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8271 (mtt180) REVERT: B 555 ILE cc_start: 0.9138 (mm) cc_final: 0.8899 (pp) REVERT: C 389 ILE cc_start: 0.8939 (mm) cc_final: 0.8475 (mm) REVERT: C 538 SER cc_start: 0.9245 (m) cc_final: 0.8929 (p) REVERT: C 583 ILE cc_start: 0.8063 (mt) cc_final: 0.7808 (mp) REVERT: D 36 ASP cc_start: 0.8151 (t70) cc_final: 0.7950 (t0) REVERT: D 609 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6822 (tm-30) outliers start: 51 outliers final: 20 residues processed: 153 average time/residue: 0.4026 time to fit residues: 74.8900 Evaluate side-chains 125 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 22 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 529 GLN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076289 restraints weight = 43454.256| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.77 r_work: 0.3068 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19984 Z= 0.145 Angle : 0.480 6.498 27357 Z= 0.260 Chirality : 0.045 0.153 3238 Planarity : 0.003 0.058 3506 Dihedral : 4.332 50.804 2922 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 3.44 % Allowed : 21.09 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2640 helix: 1.34 (0.25), residues: 489 sheet: 0.24 (0.17), residues: 891 loop : -1.08 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.014 0.001 TYR C 310 PHE 0.020 0.001 PHE B 569 TRP 0.006 0.001 TRP A 906 HIS 0.003 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00335 (19982) covalent geometry : angle 0.48016 (27353) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.07865 ( 4) hydrogen bonds : bond 0.03404 ( 613) hydrogen bonds : angle 4.77014 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 105 time to evaluate : 0.802 Fit side-chains REVERT: A 179 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8570 (m) REVERT: A 540 MET cc_start: 0.7731 (mtm) cc_final: 0.7483 (mtp) REVERT: A 960 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.5538 (tptp) REVERT: A 1011 ILE cc_start: 0.9087 (pt) cc_final: 0.8761 (pp) REVERT: B 88 ILE cc_start: 0.9247 (mm) cc_final: 0.8992 (mp) REVERT: B 251 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8412 (mtt180) REVERT: B 555 ILE cc_start: 0.9140 (mm) cc_final: 0.8903 (pp) REVERT: C 352 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 389 ILE cc_start: 0.8876 (mm) cc_final: 0.8580 (mm) REVERT: C 538 SER cc_start: 0.9256 (m) cc_final: 0.8911 (p) REVERT: C 583 ILE cc_start: 0.8016 (mt) cc_final: 0.7749 (mp) REVERT: D 36 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7964 (t0) REVERT: D 282 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8426 (t160) REVERT: D 609 GLU cc_start: 0.7584 (tm-30) cc_final: 0.6826 (tm-30) outliers start: 60 outliers final: 29 residues processed: 156 average time/residue: 0.3923 time to fit residues: 74.0678 Evaluate side-chains 133 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 95 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN B 529 GLN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076913 restraints weight = 43121.389| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.78 r_work: 0.3080 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19984 Z= 0.119 Angle : 0.467 7.195 27357 Z= 0.252 Chirality : 0.045 0.157 3238 Planarity : 0.003 0.058 3506 Dihedral : 4.244 50.665 2922 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 3.44 % Allowed : 21.43 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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 (0.17), residues: 2640 helix: 1.45 (0.25), residues: 485 sheet: 0.26 (0.17), residues: 895 loop : -1.06 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.024 0.001 TYR B 525 PHE 0.021 0.001 PHE A 810 TRP 0.006 0.001 TRP A 906 HIS 0.002 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00273 (19982) covalent geometry : angle 0.46710 (27353) SS BOND : bond 0.00101 ( 2) SS BOND : angle 1.00656 ( 4) hydrogen bonds : bond 0.03154 ( 613) hydrogen bonds : angle 4.65468 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 108 time to evaluate : 0.871 Fit side-chains REVERT: A 186 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8820 (t80) REVERT: A 540 MET cc_start: 0.7738 (mtm) cc_final: 0.7519 (mtp) REVERT: A 960 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.5556 (tptp) REVERT: A 1011 ILE cc_start: 0.9077 (pt) cc_final: 0.8762 (pp) REVERT: B 251 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8315 (mtt180) REVERT: B 555 ILE cc_start: 0.9137 (mm) cc_final: 0.8892 (pp) REVERT: C 538 SER cc_start: 0.9254 (m) cc_final: 0.8900 (p) REVERT: C 583 ILE cc_start: 0.8015 (mt) cc_final: 0.7771 (mp) REVERT: D 36 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7923 (t0) REVERT: D 282 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8484 (t0) REVERT: D 609 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6761 (tm-30) outliers start: 60 outliers final: 30 residues processed: 158 average time/residue: 0.4040 time to fit residues: 77.4388 Evaluate side-chains 135 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 442 PHE Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 40 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 78 optimal weight: 0.0370 chunk 127 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN B 180 GLN B 529 GLN C 356 GLN D 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073905 restraints weight = 43654.783| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.79 r_work: 0.3014 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19984 Z= 0.231 Angle : 0.535 7.061 27357 Z= 0.290 Chirality : 0.047 0.157 3238 Planarity : 0.004 0.059 3506 Dihedral : 4.659 51.408 2922 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 3.44 % Allowed : 21.60 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.39 (0.17), residues: 2640 helix: 1.21 (0.25), residues: 484 sheet: 0.15 (0.17), residues: 897 loop : -1.14 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.024 0.001 TYR B 525 PHE 0.025 0.002 PHE B 569 TRP 0.009 0.001 TRP A 40 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00543 (19982) covalent geometry : angle 0.53434 (27353) SS BOND : bond 0.00124 ( 2) SS BOND : angle 1.30750 ( 4) hydrogen bonds : bond 0.03940 ( 613) hydrogen bonds : angle 4.94158 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 90 time to evaluate : 0.816 Fit side-chains REVERT: A 540 MET cc_start: 0.7741 (mtm) cc_final: 0.7505 (mtp) REVERT: A 722 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7255 (mmm) REVERT: A 960 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5522 (tptp) REVERT: A 1011 ILE cc_start: 0.9053 (pt) cc_final: 0.8721 (pp) REVERT: B 106 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: B 251 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8459 (mtt180) REVERT: B 555 ILE cc_start: 0.9125 (mm) cc_final: 0.8885 (pp) REVERT: D 36 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7969 (t0) REVERT: D 282 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8495 (t0) REVERT: D 609 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6826 (tm-30) outliers start: 60 outliers final: 33 residues processed: 140 average time/residue: 0.3937 time to fit residues: 66.8531 Evaluate side-chains 126 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 442 PHE Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 133 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 258 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN C 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077034 restraints weight = 43317.036| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.79 r_work: 0.3080 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19984 Z= 0.105 Angle : 0.467 6.910 27357 Z= 0.253 Chirality : 0.045 0.157 3238 Planarity : 0.003 0.059 3506 Dihedral : 4.275 49.960 2922 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.87 % Allowed : 22.23 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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 (0.17), residues: 2640 helix: 1.51 (0.25), residues: 484 sheet: 0.22 (0.17), residues: 887 loop : -1.05 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 127 TYR 0.022 0.001 TYR B 525 PHE 0.020 0.001 PHE B 286 TRP 0.007 0.001 TRP A 282 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00235 (19982) covalent geometry : angle 0.46651 (27353) SS BOND : bond 0.00089 ( 2) SS BOND : angle 1.15160 ( 4) hydrogen bonds : bond 0.03044 ( 613) hydrogen bonds : angle 4.63254 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.784 Fit side-chains REVERT: A 186 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8864 (t80) REVERT: A 540 MET cc_start: 0.7738 (mtm) cc_final: 0.7523 (mtp) REVERT: A 960 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5383 (tptp) REVERT: A 1011 ILE cc_start: 0.9073 (pt) cc_final: 0.8766 (pp) REVERT: B 140 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: B 251 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8290 (mtt180) REVERT: B 554 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 555 ILE cc_start: 0.9134 (mm) cc_final: 0.8852 (pp) REVERT: D 36 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7958 (t0) REVERT: D 282 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8495 (t0) REVERT: D 609 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6808 (tm-30) outliers start: 50 outliers final: 31 residues processed: 144 average time/residue: 0.4003 time to fit residues: 69.6262 Evaluate side-chains 133 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 124 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 582 ASN C 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.074256 restraints weight = 43601.878| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.78 r_work: 0.3022 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19984 Z= 0.212 Angle : 0.524 6.918 27357 Z= 0.284 Chirality : 0.046 0.153 3238 Planarity : 0.003 0.059 3506 Dihedral : 4.581 50.810 2922 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 2.98 % Allowed : 22.18 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.36 (0.17), residues: 2640 helix: 1.23 (0.25), residues: 490 sheet: 0.17 (0.17), residues: 898 loop : -1.14 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.022 0.001 TYR B 525 PHE 0.024 0.002 PHE B 569 TRP 0.008 0.001 TRP A 40 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00496 (19982) covalent geometry : angle 0.52418 (27353) SS BOND : bond 0.00104 ( 2) SS BOND : angle 1.32601 ( 4) hydrogen bonds : bond 0.03760 ( 613) hydrogen bonds : angle 4.84307 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 0.867 Fit side-chains REVERT: A 540 MET cc_start: 0.7733 (mtm) cc_final: 0.7513 (mtp) REVERT: A 960 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5335 (tptp) REVERT: A 1011 ILE cc_start: 0.9032 (pt) cc_final: 0.8718 (pp) REVERT: B 88 ILE cc_start: 0.9124 (mm) cc_final: 0.8876 (mp) REVERT: B 106 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: B 251 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8380 (mtt180) REVERT: B 554 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7654 (t0) REVERT: B 555 ILE cc_start: 0.9127 (mm) cc_final: 0.8861 (pp) REVERT: D 36 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7966 (t0) REVERT: D 282 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8480 (t0) REVERT: D 609 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6762 (tm-30) outliers start: 52 outliers final: 30 residues processed: 135 average time/residue: 0.4016 time to fit residues: 65.8195 Evaluate side-chains 126 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 241 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 210 optimal weight: 40.0000 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN C 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077652 restraints weight = 42773.771| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.78 r_work: 0.3096 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19984 Z= 0.094 Angle : 0.466 6.921 27357 Z= 0.251 Chirality : 0.045 0.161 3238 Planarity : 0.003 0.059 3506 Dihedral : 4.201 49.280 2922 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.06 % Allowed : 22.98 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -0.14 (0.17), residues: 2640 helix: 1.60 (0.25), residues: 484 sheet: 0.26 (0.17), residues: 886 loop : -1.02 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 45 TYR 0.020 0.001 TYR B 525 PHE 0.013 0.001 PHE B 293 TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00208 (19982) covalent geometry : angle 0.46596 (27353) SS BOND : bond 0.00086 ( 2) SS BOND : angle 1.13476 ( 4) hydrogen bonds : bond 0.02905 ( 613) hydrogen bonds : angle 4.56115 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.843 Fit side-chains REVERT: A 540 MET cc_start: 0.7738 (mtm) cc_final: 0.7538 (mtp) REVERT: A 679 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: A 960 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5371 (tptp) REVERT: A 1011 ILE cc_start: 0.9062 (pt) cc_final: 0.8782 (pp) REVERT: B 88 ILE cc_start: 0.9170 (mm) cc_final: 0.8919 (mp) REVERT: B 140 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: B 251 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8267 (mtt180) REVERT: B 554 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 555 ILE cc_start: 0.9123 (mm) cc_final: 0.8845 (pp) REVERT: D 36 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7955 (t0) REVERT: D 282 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8488 (t0) REVERT: D 609 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6745 (tm-30) outliers start: 36 outliers final: 22 residues processed: 134 average time/residue: 0.4236 time to fit residues: 68.3876 Evaluate side-chains 125 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 81 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 chunk 153 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN C 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.076969 restraints weight = 43142.124| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.78 r_work: 0.3080 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19984 Z= 0.118 Angle : 0.473 7.190 27357 Z= 0.254 Chirality : 0.045 0.161 3238 Planarity : 0.003 0.059 3506 Dihedral : 4.046 34.809 2920 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.29 % Allowed : 22.92 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2640 helix: 1.58 (0.25), residues: 485 sheet: 0.30 (0.17), residues: 898 loop : -1.00 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.020 0.001 TYR B 525 PHE 0.024 0.001 PHE A 810 TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00271 (19982) covalent geometry : angle 0.47277 (27353) SS BOND : bond 0.00096 ( 2) SS BOND : angle 1.07819 ( 4) hydrogen bonds : bond 0.03058 ( 613) hydrogen bonds : angle 4.56534 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.539 Fit side-chains REVERT: A 382 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 540 MET cc_start: 0.7784 (mtm) cc_final: 0.7558 (mtp) REVERT: A 679 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6618 (mm-40) REVERT: A 960 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.5548 (tptp) REVERT: A 1011 ILE cc_start: 0.9051 (pt) cc_final: 0.8764 (pp) REVERT: B 88 ILE cc_start: 0.9185 (mm) cc_final: 0.8927 (mp) REVERT: B 251 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8296 (mtt180) REVERT: B 554 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7560 (t0) REVERT: B 555 ILE cc_start: 0.9130 (mm) cc_final: 0.8855 (pp) REVERT: D 36 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7997 (t0) REVERT: D 282 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8491 (t0) REVERT: D 609 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6713 (tm-30) outliers start: 40 outliers final: 27 residues processed: 134 average time/residue: 0.3652 time to fit residues: 58.9623 Evaluate side-chains 130 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 942 ILE Chi-restraints excluded: chain A residue 960 LYS Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 442 PHE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 442 PHE Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 610 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 62 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN C 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073952 restraints weight = 43815.636| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.80 r_work: 0.3015 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19984 Z= 0.228 Angle : 0.538 8.815 27357 Z= 0.291 Chirality : 0.047 0.159 3238 Planarity : 0.003 0.059 3506 Dihedral : 4.468 38.791 2920 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 2.29 % Allowed : 22.92 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2640 helix: 1.23 (0.24), residues: 490 sheet: 0.21 (0.17), residues: 898 loop : -1.11 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.021 0.001 TYR B 525 PHE 0.026 0.002 PHE A 810 TRP 0.009 0.001 TRP A 40 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00534 (19982) covalent geometry : angle 0.53765 (27353) SS BOND : bond 0.00138 ( 2) SS BOND : angle 1.25626 ( 4) hydrogen bonds : bond 0.03839 ( 613) hydrogen bonds : angle 4.84410 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5810.49 seconds wall clock time: 99 minutes 56.19 seconds (5996.19 seconds total)