Starting phenix.real_space_refine on Mon May 4 01:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvv_67303/05_2026/9xvv_67303.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.053 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 91 5.16 5 C 10686 2.51 5 N 2819 2.21 5 O 3167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16763 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5787 Classifications: {'peptide': 717} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 680} Chain: "C" Number of atoms: 6237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6237 Classifications: {'peptide': 787} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 742} Chain: "B" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4662 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 545} Chain breaks: 7 Chain: "F" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Unusual residues: {'GLC': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.91, per 1000 atoms: 0.23 Number of scatterers: 16763 At special positions: 0 Unit cell: (98.88, 101.76, 236.16, 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 91 16.00 O 3167 8.00 N 2819 7.00 C 10686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC F 1 " - " GLC F 2 " " GLC F 2 " - " GLC F 3 " " GLC F 3 " - " GLC F 4 " " GLC F 4 " - " GLC F 5 " " GLC F 5 " - " GLC F 6 " " GLC F 6 " - " GLC F 7 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 741.6 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 25 sheets defined 24.4% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.217A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.687A pdb=" N ASN A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 removed outlier: 4.118A pdb=" N ASN A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N SER A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 360 removed outlier: 3.647A pdb=" N GLN A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.673A pdb=" N TRP A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.595A pdb=" N ARG A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 537 through 557 removed outlier: 3.675A pdb=" N ARG A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.889A pdb=" N LEU C 294 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.869A pdb=" N ALA C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 320 through 326' Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 372 through 388 removed outlier: 4.210A pdb=" N ASN C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 427 removed outlier: 3.972A pdb=" N LYS C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 453 Processing helix chain 'C' and resid 461 through 467 Processing helix chain 'C' and resid 477 through 485 Processing helix chain 'C' and resid 522 through 533 removed outlier: 3.633A pdb=" N ARG C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.519A pdb=" N CYS C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.950A pdb=" N VAL C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 621 removed outlier: 5.347A pdb=" N ARG C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 646 removed outlier: 4.080A pdb=" N ARG C 646 " --> pdb=" O LEU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 676 removed outlier: 3.734A pdb=" N SER C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 673 " --> pdb=" O MET C 669 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.674A pdb=" N ARG B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 removed outlier: 4.221A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 198 through 205 removed outlier: 4.145A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.810A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.550A pdb=" N PHE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.725A pdb=" N TRP B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 446 through 459 removed outlier: 4.081A pdb=" N ARG B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 473 Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 537 through 558 Processing helix chain 'B' and resid 579 through 583 removed outlier: 4.271A pdb=" N CYS B 582 " --> pdb=" O ASN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 602 through 616 removed outlier: 3.548A pdb=" N ASP B 614 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 719 removed outlier: 3.930A pdb=" N GLN B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE B 716 " --> pdb=" O GLN B 712 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 719 " --> pdb=" O HIS B 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.717A pdb=" N SER A 54 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 150 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.419A pdb=" N TYR A 178 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 289 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ARG A 365 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET A 291 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 420 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TRP A 445 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA A 422 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 444 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 490 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 177 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.036A pdb=" N SER A 254 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 633 removed outlier: 3.990A pdb=" N ALA A 650 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 660 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER A 729 " --> pdb=" O ASP A 689 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP A 689 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 731 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 31 Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 31 Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 206 Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.520A pdb=" N GLY C 271 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 299 removed outlier: 3.549A pdb=" N GLY C 456 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER C 561 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL C 626 " --> pdb=" O SER C 561 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN C 563 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN C 628 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 691 through 694 removed outlier: 7.066A pdb=" N CYS C 802 " --> pdb=" O ASP C 767 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP C 767 " --> pdb=" O CYS C 802 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 804 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 749 through 752 Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.667A pdb=" N SER B 46 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AC2, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.683A pdb=" N CYS B 151 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 150 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 177 through 180 removed outlier: 3.568A pdb=" N TYR B 178 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 420 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TRP B 445 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA B 422 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 444 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 564 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 225 removed outlier: 6.869A pdb=" N GLU B 224 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.776A pdb=" N SER B 232 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 630 through 633 removed outlier: 4.822A pdb=" N GLU B 660 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER B 729 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 689 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 731 " --> pdb=" O PHE B 687 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 672 through 675 519 hydrogen bonds defined for protein. 1377 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: 3.30 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5252 1.34 - 1.45: 2981 1.45 - 1.57: 8845 1.57 - 1.69: 1 1.69 - 1.81: 139 Bond restraints: 17218 Sorted by residual: bond pdb=" C1 GLC F 5 " pdb=" O5 GLC F 5 " ideal model delta sigma weight residual 1.402 1.509 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C1 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.402 1.507 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C1 GLC F 3 " pdb=" O5 GLC F 3 " ideal model delta sigma weight residual 1.402 1.503 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 GLC F 4 " pdb=" O5 GLC F 4 " ideal model delta sigma weight residual 1.402 1.501 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C1 GLC F 6 " pdb=" O5 GLC F 6 " ideal model delta sigma weight residual 1.402 1.499 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 23165 3.22 - 6.44: 161 6.44 - 9.66: 12 9.66 - 12.88: 1 12.88 - 16.10: 1 Bond angle restraints: 23340 Sorted by residual: angle pdb=" N ASN B 518 " pdb=" CA ASN B 518 " pdb=" C ASN B 518 " ideal model delta sigma weight residual 114.31 98.21 16.10 1.29e+00 6.01e-01 1.56e+02 angle pdb=" N LEU C 604 " pdb=" CA LEU C 604 " pdb=" C LEU C 604 " ideal model delta sigma weight residual 114.62 107.59 7.03 1.14e+00 7.69e-01 3.80e+01 angle pdb=" C LEU B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta sigma weight residual 120.68 127.87 -7.19 1.52e+00 4.33e-01 2.24e+01 angle pdb=" N GLY B 520 " pdb=" CA GLY B 520 " pdb=" C GLY B 520 " ideal model delta sigma weight residual 113.18 102.72 10.46 2.37e+00 1.78e-01 1.95e+01 angle pdb=" N ARG B 187 " pdb=" CA ARG B 187 " pdb=" C ARG B 187 " ideal model delta sigma weight residual 114.56 109.18 5.38 1.27e+00 6.20e-01 1.80e+01 ... (remaining 23335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 9198 25.69 - 51.37: 863 51.37 - 77.06: 97 77.06 - 102.75: 48 102.75 - 128.44: 35 Dihedral angle restraints: 10241 sinusoidal: 4220 harmonic: 6021 Sorted by residual: dihedral pdb=" CA ALA B 271 " pdb=" C ALA B 271 " pdb=" N ILE B 272 " pdb=" CA ILE B 272 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR C 225 " pdb=" C THR C 225 " pdb=" N TRP C 226 " pdb=" CA TRP C 226 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLY C 774 " pdb=" C GLY C 774 " pdb=" N PHE C 775 " pdb=" CA PHE C 775 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 10238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1533 0.041 - 0.082: 708 0.082 - 0.123: 203 0.123 - 0.164: 32 0.164 - 0.205: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" C4 GLC F 6 " pdb=" C3 GLC F 6 " pdb=" C5 GLC F 6 " pdb=" O4 GLC F 6 " both_signs ideal model delta sigma weight residual False -2.50 -2.29 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE C 775 " pdb=" N PHE C 775 " pdb=" C PHE C 775 " pdb=" CB PHE C 775 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 2475 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 122 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO C 123 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 647 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO C 648 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 648 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 648 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 172 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C GLN A 172 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN A 172 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 173 " 0.013 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5303 2.83 - 3.35: 14114 3.35 - 3.87: 26860 3.87 - 4.38: 32175 4.38 - 4.90: 54569 Nonbonded interactions: 133021 Sorted by model distance: nonbonded pdb=" N ASN B 518 " pdb=" N ASP B 519 " model vdw 2.314 2.560 nonbonded pdb=" O4 GLC F 3 " pdb=" O2 GLC F 4 " model vdw 2.431 2.432 nonbonded pdb=" N GLU C 283 " pdb=" OE1 GLU C 283 " model vdw 2.463 3.120 nonbonded pdb=" C4 GLC F 3 " pdb=" O6 GLC F 3 " model vdw 2.472 2.776 nonbonded pdb=" N GLU B 707 " pdb=" OE1 GLU B 707 " model vdw 2.495 3.120 ... (remaining 133016 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.720 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 17224 Z= 0.278 Angle : 0.751 16.105 23358 Z= 0.410 Chirality : 0.049 0.205 2478 Planarity : 0.005 0.061 3024 Dihedral : 21.230 128.435 6371 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.44 % Favored : 90.32 % Rotamer: Outliers : 3.69 % Allowed : 27.58 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 2056 helix: -0.85 (0.24), residues: 430 sheet: -0.54 (0.24), residues: 443 loop : -1.90 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 683 TYR 0.020 0.002 TYR B 102 PHE 0.028 0.002 PHE B 651 TRP 0.015 0.002 TRP C 517 HIS 0.007 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00605 (17218) covalent geometry : angle 0.74731 (23340) hydrogen bonds : bond 0.21762 ( 491) hydrogen bonds : angle 7.61843 ( 1377) link_ALPHA1-4 : bond 0.00888 ( 6) link_ALPHA1-4 : angle 2.78404 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.6652 (ttm170) cc_final: 0.6208 (ttm110) REVERT: A 26 ILE cc_start: 0.7609 (tt) cc_final: 0.7360 (tt) REVERT: A 92 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7492 (ttt180) REVERT: A 189 GLU cc_start: 0.7141 (mp0) cc_final: 0.6914 (mp0) REVERT: A 285 ARG cc_start: 0.8429 (mtt90) cc_final: 0.7844 (mmm160) REVERT: A 358 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8496 (mm-30) REVERT: A 416 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7582 (ptp-170) REVERT: A 611 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8360 (ttmt) REVERT: A 614 ASP cc_start: 0.8611 (t0) cc_final: 0.8342 (t0) REVERT: A 683 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7473 (ptt90) REVERT: C 92 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6136 (tp-100) REVERT: C 118 ASP cc_start: 0.7157 (t0) cc_final: 0.6740 (m-30) REVERT: C 248 GLU cc_start: 0.1974 (OUTLIER) cc_final: 0.0795 (mt-10) REVERT: C 278 SER cc_start: 0.6806 (OUTLIER) cc_final: 0.6555 (t) REVERT: C 504 MET cc_start: 0.6946 (tpp) cc_final: 0.6530 (mpp) REVERT: C 567 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7306 (mtp85) REVERT: C 579 PHE cc_start: 0.7751 (m-80) cc_final: 0.7486 (m-80) REVERT: C 802 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7494 (p) REVERT: B 100 TYR cc_start: 0.5808 (p90) cc_final: 0.5498 (p90) REVERT: B 125 PRO cc_start: 0.6232 (Cg_exo) cc_final: 0.6007 (Cg_endo) REVERT: B 290 ILE cc_start: 0.7696 (mt) cc_final: 0.7408 (tt) REVERT: B 563 MET cc_start: 0.7434 (tmm) cc_final: 0.7111 (tpp) REVERT: B 587 MET cc_start: 0.8216 (mtp) cc_final: 0.7979 (ttm) REVERT: B 631 GLN cc_start: 0.7221 (tp40) cc_final: 0.6760 (tp-100) outliers start: 68 outliers final: 27 residues processed: 329 average time/residue: 0.6748 time to fit residues: 244.5954 Evaluate side-chains 228 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 694 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0570 chunk 200 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 ASN C 161 HIS ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 518 ASN B 678 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.199852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154166 restraints weight = 19030.764| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.34 r_work: 0.3620 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17224 Z= 0.117 Angle : 0.635 9.233 23358 Z= 0.320 Chirality : 0.045 0.263 2478 Planarity : 0.005 0.053 3024 Dihedral : 15.138 112.276 2454 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.07 % Favored : 91.73 % Rotamer: Outliers : 4.34 % Allowed : 25.62 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2056 helix: 0.01 (0.25), residues: 440 sheet: -0.26 (0.24), residues: 433 loop : -1.84 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 683 TYR 0.016 0.001 TYR B 233 PHE 0.016 0.001 PHE B 651 TRP 0.015 0.001 TRP C 448 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00252 (17218) covalent geometry : angle 0.62885 (23340) hydrogen bonds : bond 0.04488 ( 491) hydrogen bonds : angle 5.53092 ( 1377) link_ALPHA1-4 : bond 0.01404 ( 6) link_ALPHA1-4 : angle 3.23984 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7394 (tt) cc_final: 0.7149 (tt) REVERT: A 92 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7412 (ttt180) REVERT: A 105 ASP cc_start: 0.8238 (t0) cc_final: 0.8036 (t0) REVERT: A 135 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 172 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: A 285 ARG cc_start: 0.8529 (mtt90) cc_final: 0.7935 (mmm160) REVERT: A 326 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: A 358 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: A 521 GLU cc_start: 0.7486 (tp30) cc_final: 0.7230 (tp30) REVERT: A 594 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7765 (mttp) REVERT: A 611 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8407 (ttmt) REVERT: A 614 ASP cc_start: 0.8742 (t70) cc_final: 0.8508 (t0) REVERT: A 683 ARG cc_start: 0.7515 (ptm160) cc_final: 0.7048 (ptt90) REVERT: C 56 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 100 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: C 248 GLU cc_start: 0.2018 (OUTLIER) cc_final: 0.0846 (mt-10) REVERT: C 284 ASP cc_start: 0.7953 (t70) cc_final: 0.7549 (t70) REVERT: C 504 MET cc_start: 0.6771 (tpp) cc_final: 0.6274 (mpp) REVERT: C 567 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7078 (mtp85) REVERT: C 802 CYS cc_start: 0.7486 (m) cc_final: 0.6797 (p) REVERT: B 149 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5010 (mmt) REVERT: B 166 MET cc_start: 0.3149 (tpp) cc_final: 0.2928 (tmm) REVERT: B 187 ARG cc_start: 0.6281 (mmp-170) cc_final: 0.5893 (mmp-170) REVERT: B 252 PHE cc_start: 0.6878 (m-80) cc_final: 0.6436 (m-80) REVERT: B 256 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.5372 (tmt) REVERT: B 290 ILE cc_start: 0.7036 (mt) cc_final: 0.6373 (tt) REVERT: B 563 MET cc_start: 0.7599 (tmm) cc_final: 0.7324 (ttp) REVERT: B 611 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7249 (tttm) outliers start: 80 outliers final: 18 residues processed: 273 average time/residue: 0.6460 time to fit residues: 195.3608 Evaluate side-chains 212 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 270 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 ASN A 528 ASN C 161 HIS C 307 HIS ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.196130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147763 restraints weight = 19149.424| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.22 r_work: 0.3560 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17224 Z= 0.163 Angle : 0.673 10.142 23358 Z= 0.343 Chirality : 0.047 0.216 2478 Planarity : 0.005 0.062 3024 Dihedral : 12.622 109.633 2416 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.95 % Favored : 90.86 % Rotamer: Outliers : 5.10 % Allowed : 25.24 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2056 helix: 0.03 (0.25), residues: 450 sheet: -0.23 (0.24), residues: 434 loop : -1.80 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 308 TYR 0.016 0.002 TYR B 581 PHE 0.026 0.002 PHE B 651 TRP 0.015 0.002 TRP A 87 HIS 0.005 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00369 (17218) covalent geometry : angle 0.66800 (23340) hydrogen bonds : bond 0.05526 ( 491) hydrogen bonds : angle 5.50261 ( 1377) link_ALPHA1-4 : bond 0.01544 ( 6) link_ALPHA1-4 : angle 3.08665 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 197 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7771 (tt) cc_final: 0.7519 (tt) REVERT: A 92 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7500 (ttt180) REVERT: A 135 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: A 258 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8696 (mtm180) REVERT: A 358 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: A 611 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8519 (ttmt) REVERT: A 614 ASP cc_start: 0.8750 (t0) cc_final: 0.8497 (t0) REVERT: A 683 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7165 (ptt90) REVERT: C 92 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5900 (tp-100) REVERT: C 93 ASP cc_start: 0.5594 (t0) cc_final: 0.5365 (t0) REVERT: C 100 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: C 224 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.6352 (m-40) REVERT: C 248 GLU cc_start: 0.2364 (OUTLIER) cc_final: 0.1149 (mt-10) REVERT: C 284 ASP cc_start: 0.7969 (t70) cc_final: 0.7469 (t0) REVERT: C 308 ARG cc_start: 0.6571 (tpm170) cc_final: 0.6120 (ttm-80) REVERT: C 365 TYR cc_start: 0.8254 (m-10) cc_final: 0.8021 (m-10) REVERT: C 378 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6561 (ttt) REVERT: C 504 MET cc_start: 0.6796 (tpp) cc_final: 0.6332 (mpp) REVERT: C 567 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7056 (mtp85) REVERT: C 583 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6597 (pt0) REVERT: C 635 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5813 (pp) REVERT: B 187 ARG cc_start: 0.6396 (mmp-170) cc_final: 0.5998 (mmp-170) REVERT: B 240 HIS cc_start: 0.5470 (OUTLIER) cc_final: 0.4608 (m-70) REVERT: B 252 PHE cc_start: 0.6833 (m-80) cc_final: 0.6411 (m-80) REVERT: B 256 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.5502 (tmt) REVERT: B 563 MET cc_start: 0.7659 (tmm) cc_final: 0.7356 (ttp) REVERT: B 611 LYS cc_start: 0.7780 (ttpp) cc_final: 0.7343 (tttm) REVERT: B 615 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6324 (mt-10) outliers start: 94 outliers final: 33 residues processed: 273 average time/residue: 0.6584 time to fit residues: 199.4063 Evaluate side-chains 230 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 11 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN A 528 ASN A 678 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.197698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151009 restraints weight = 19031.441| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.20 r_work: 0.3590 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17224 Z= 0.124 Angle : 0.614 9.583 23358 Z= 0.312 Chirality : 0.045 0.203 2478 Planarity : 0.004 0.055 3024 Dihedral : 10.690 101.784 2413 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.12 % Rotamer: Outliers : 4.83 % Allowed : 24.97 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2056 helix: 0.27 (0.25), residues: 442 sheet: -0.24 (0.24), residues: 441 loop : -1.77 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 285 TYR 0.011 0.001 TYR A 178 PHE 0.022 0.001 PHE B 651 TRP 0.012 0.001 TRP A 87 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00273 (17218) covalent geometry : angle 0.60769 (23340) hydrogen bonds : bond 0.04228 ( 491) hydrogen bonds : angle 5.23941 ( 1377) link_ALPHA1-4 : bond 0.01556 ( 6) link_ALPHA1-4 : angle 3.22334 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 184 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 358 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8599 (mp0) REVERT: A 611 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8496 (ttmt) REVERT: A 614 ASP cc_start: 0.8733 (t0) cc_final: 0.8496 (t0) REVERT: A 683 ARG cc_start: 0.7498 (ptm160) cc_final: 0.7033 (ptt90) REVERT: C 68 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.5873 (pt) REVERT: C 92 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.5857 (tp-100) REVERT: C 93 ASP cc_start: 0.5509 (t0) cc_final: 0.5250 (t0) REVERT: C 100 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: C 118 ASP cc_start: 0.7020 (t0) cc_final: 0.6383 (m-30) REVERT: C 200 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6135 (tttm) REVERT: C 248 GLU cc_start: 0.2349 (OUTLIER) cc_final: 0.1120 (mt-10) REVERT: C 302 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7284 (tttp) REVERT: C 365 TYR cc_start: 0.8192 (m-10) cc_final: 0.7946 (m-10) REVERT: C 378 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.6507 (ttt) REVERT: C 504 MET cc_start: 0.6824 (tpp) cc_final: 0.6411 (mpp) REVERT: C 583 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6543 (pt0) REVERT: C 635 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5792 (pp) REVERT: C 787 GLU cc_start: 0.2268 (OUTLIER) cc_final: 0.0860 (tp30) REVERT: B 128 LYS cc_start: 0.6931 (mmtt) cc_final: 0.6705 (mptt) REVERT: B 149 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.4804 (mmt) REVERT: B 166 MET cc_start: 0.3147 (tpp) cc_final: 0.2864 (tmm) REVERT: B 187 ARG cc_start: 0.6343 (mmp-170) cc_final: 0.5970 (mmp-170) REVERT: B 252 PHE cc_start: 0.6763 (m-80) cc_final: 0.6366 (m-80) REVERT: B 256 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.5526 (tmt) REVERT: B 259 TYR cc_start: 0.6859 (m-10) cc_final: 0.5909 (m-10) REVERT: B 469 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6606 (pt0) REVERT: B 611 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7340 (tttm) outliers start: 89 outliers final: 37 residues processed: 254 average time/residue: 0.6644 time to fit residues: 186.7070 Evaluate side-chains 228 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 743 ASN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 168 optimal weight: 0.6980 chunk 159 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 678 ASN C 161 HIS C 527 ASN C 698 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.193616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142753 restraints weight = 18862.056| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.99 r_work: 0.3546 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17224 Z= 0.211 Angle : 0.715 8.233 23358 Z= 0.371 Chirality : 0.049 0.253 2478 Planarity : 0.006 0.058 3024 Dihedral : 10.567 101.815 2413 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.39 % Favored : 90.42 % Rotamer: Outliers : 5.75 % Allowed : 24.38 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2056 helix: 0.10 (0.25), residues: 433 sheet: -0.34 (0.24), residues: 432 loop : -1.79 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 183 TYR 0.024 0.002 TYR B 581 PHE 0.029 0.002 PHE B 651 TRP 0.019 0.002 TRP A 87 HIS 0.006 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00489 (17218) covalent geometry : angle 0.71095 (23340) hydrogen bonds : bond 0.06098 ( 491) hydrogen bonds : angle 5.56794 ( 1377) link_ALPHA1-4 : bond 0.01508 ( 6) link_ALPHA1-4 : angle 2.91405 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 190 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8157 (mtm110) REVERT: A 135 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 187 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8094 (tmt-80) REVERT: A 358 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: A 611 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8500 (ttmt) REVERT: A 614 ASP cc_start: 0.8723 (t0) cc_final: 0.8499 (t0) REVERT: A 683 ARG cc_start: 0.7651 (ptm160) cc_final: 0.7202 (ptt90) REVERT: C 92 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5846 (tp-100) REVERT: C 93 ASP cc_start: 0.5723 (t0) cc_final: 0.5433 (t0) REVERT: C 100 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: C 200 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6110 (tttm) REVERT: C 248 GLU cc_start: 0.2385 (OUTLIER) cc_final: 0.1194 (mt-10) REVERT: C 284 ASP cc_start: 0.7948 (t70) cc_final: 0.7271 (t0) REVERT: C 302 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7202 (tttp) REVERT: C 365 TYR cc_start: 0.8264 (m-10) cc_final: 0.7997 (m-10) REVERT: C 378 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.6724 (ttt) REVERT: C 504 MET cc_start: 0.6990 (tpp) cc_final: 0.6608 (mpp) REVERT: C 635 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5690 (pp) REVERT: C 787 GLU cc_start: 0.2608 (OUTLIER) cc_final: 0.1127 (tp30) REVERT: B 37 THR cc_start: 0.1055 (OUTLIER) cc_final: 0.0640 (p) REVERT: B 40 ASP cc_start: 0.3492 (OUTLIER) cc_final: 0.3257 (p0) REVERT: B 149 MET cc_start: 0.5960 (OUTLIER) cc_final: 0.4599 (mmt) REVERT: B 187 ARG cc_start: 0.6318 (mmp-170) cc_final: 0.5900 (mmp-170) REVERT: B 208 HIS cc_start: 0.6306 (t70) cc_final: 0.5596 (t70) REVERT: B 256 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.5896 (tmt) REVERT: B 259 TYR cc_start: 0.7124 (m-10) cc_final: 0.6342 (m-10) REVERT: B 408 MET cc_start: -0.1339 (OUTLIER) cc_final: -0.2454 (mmm) REVERT: B 469 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6661 (pt0) REVERT: B 611 LYS cc_start: 0.7767 (ttpp) cc_final: 0.6797 (tttm) REVERT: B 615 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6008 (mp0) outliers start: 106 outliers final: 45 residues processed: 273 average time/residue: 0.6258 time to fit residues: 190.0539 Evaluate side-chains 249 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 188 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 528 ASN A 678 ASN C 161 HIS C 376 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 360 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.194538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146897 restraints weight = 18923.187| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.32 r_work: 0.3544 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17224 Z= 0.166 Angle : 0.665 9.600 23358 Z= 0.345 Chirality : 0.047 0.191 2478 Planarity : 0.005 0.057 3024 Dihedral : 10.175 103.583 2413 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.51 % Favored : 91.29 % Rotamer: Outliers : 5.21 % Allowed : 25.24 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2056 helix: 0.17 (0.25), residues: 431 sheet: -0.32 (0.24), residues: 429 loop : -1.80 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 67 TYR 0.014 0.002 TYR B 581 PHE 0.024 0.002 PHE B 651 TRP 0.016 0.002 TRP A 87 HIS 0.005 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00378 (17218) covalent geometry : angle 0.66044 (23340) hydrogen bonds : bond 0.05147 ( 491) hydrogen bonds : angle 5.45048 ( 1377) link_ALPHA1-4 : bond 0.01647 ( 6) link_ALPHA1-4 : angle 2.91696 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 183 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8136 (mtm110) REVERT: A 135 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 187 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8046 (tmt-80) REVERT: A 358 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: A 611 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8541 (ttmt) REVERT: A 614 ASP cc_start: 0.8764 (t0) cc_final: 0.8522 (t0) REVERT: A 683 ARG cc_start: 0.7680 (ptm160) cc_final: 0.7229 (ptt90) REVERT: C 92 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.5821 (tp-100) REVERT: C 93 ASP cc_start: 0.5675 (t0) cc_final: 0.5327 (t0) REVERT: C 100 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: C 200 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6092 (tttm) REVERT: C 302 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7251 (tttp) REVERT: C 308 ARG cc_start: 0.6696 (tpm-80) cc_final: 0.6287 (tpp-160) REVERT: C 365 TYR cc_start: 0.8259 (m-10) cc_final: 0.7980 (m-10) REVERT: C 378 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6785 (ttt) REVERT: C 635 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5702 (pp) REVERT: C 787 GLU cc_start: 0.2544 (OUTLIER) cc_final: 0.1126 (tp30) REVERT: B 149 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.4524 (mmt) REVERT: B 166 MET cc_start: 0.3282 (tpp) cc_final: 0.2816 (tmm) REVERT: B 187 ARG cc_start: 0.6389 (mmp-170) cc_final: 0.5984 (mmp-170) REVERT: B 256 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.5823 (tmt) REVERT: B 259 TYR cc_start: 0.7229 (m-10) cc_final: 0.6479 (m-10) REVERT: B 408 MET cc_start: -0.1117 (OUTLIER) cc_final: -0.2153 (mmm) REVERT: B 469 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6713 (pt0) REVERT: B 611 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7345 (tttm) outliers start: 96 outliers final: 48 residues processed: 258 average time/residue: 0.6438 time to fit residues: 184.3429 Evaluate side-chains 241 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 3 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 585 ASN A 678 ASN C 161 HIS B 273 ASN B 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141752 restraints weight = 18872.589| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.24 r_work: 0.3525 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17224 Z= 0.211 Angle : 0.726 7.647 23358 Z= 0.379 Chirality : 0.049 0.210 2478 Planarity : 0.006 0.059 3024 Dihedral : 10.281 104.192 2410 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.12 % Favored : 89.69 % Rotamer: Outliers : 5.05 % Allowed : 25.41 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2056 helix: -0.03 (0.25), residues: 435 sheet: -0.39 (0.24), residues: 434 loop : -1.79 (0.16), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 133 TYR 0.021 0.002 TYR B 581 PHE 0.028 0.002 PHE B 651 TRP 0.023 0.002 TRP A 445 HIS 0.006 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00487 (17218) covalent geometry : angle 0.72188 (23340) hydrogen bonds : bond 0.06138 ( 491) hydrogen bonds : angle 5.63737 ( 1377) link_ALPHA1-4 : bond 0.01503 ( 6) link_ALPHA1-4 : angle 2.93438 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 181 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (mtm110) REVERT: A 96 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7387 (tttt) REVERT: A 135 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 187 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (tmt-80) REVERT: A 358 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: A 432 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: A 611 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8513 (ttmt) REVERT: A 614 ASP cc_start: 0.8747 (t0) cc_final: 0.8513 (t0) REVERT: A 683 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7265 (ptt90) REVERT: A 705 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 92 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5700 (tp-100) REVERT: C 93 ASP cc_start: 0.5537 (t0) cc_final: 0.5125 (t0) REVERT: C 100 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: C 200 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6172 (tttm) REVERT: C 284 ASP cc_start: 0.8096 (t70) cc_final: 0.7521 (t0) REVERT: C 302 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7156 (tttp) REVERT: C 308 ARG cc_start: 0.6678 (tpm-80) cc_final: 0.6312 (tpp-160) REVERT: C 365 TYR cc_start: 0.8237 (m-10) cc_final: 0.7942 (m-10) REVERT: C 378 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6752 (ttt) REVERT: C 787 GLU cc_start: 0.2637 (OUTLIER) cc_final: 0.1214 (tp30) REVERT: B 40 ASP cc_start: 0.3564 (OUTLIER) cc_final: 0.3257 (p0) REVERT: B 149 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.4437 (mmt) REVERT: B 206 LEU cc_start: 0.5316 (mt) cc_final: 0.5103 (mp) REVERT: B 252 PHE cc_start: 0.6683 (m-80) cc_final: 0.6258 (m-80) REVERT: B 292 ASP cc_start: 0.4034 (OUTLIER) cc_final: 0.3734 (t0) REVERT: B 595 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6768 (tptp) REVERT: B 597 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: B 615 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5807 (mp0) outliers start: 93 outliers final: 50 residues processed: 252 average time/residue: 0.6427 time to fit residues: 179.8806 Evaluate side-chains 246 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 0.0470 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 141 optimal weight: 0.0570 chunk 177 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 528 ASN C 161 HIS C 376 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151459 restraints weight = 19058.152| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.15 r_work: 0.3602 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17224 Z= 0.109 Angle : 0.588 11.038 23358 Z= 0.302 Chirality : 0.043 0.165 2478 Planarity : 0.004 0.054 3024 Dihedral : 9.725 103.761 2408 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.49 % Favored : 92.32 % Rotamer: Outliers : 3.31 % Allowed : 27.47 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 2056 helix: 0.42 (0.26), residues: 436 sheet: -0.20 (0.24), residues: 430 loop : -1.69 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 67 TYR 0.011 0.001 TYR A 231 PHE 0.017 0.001 PHE B 651 TRP 0.020 0.001 TRP A 445 HIS 0.004 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00235 (17218) covalent geometry : angle 0.58290 (23340) hydrogen bonds : bond 0.03471 ( 491) hydrogen bonds : angle 5.13078 ( 1377) link_ALPHA1-4 : bond 0.01720 ( 6) link_ALPHA1-4 : angle 2.82623 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 187 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (tmt-80) REVERT: A 326 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 358 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: A 611 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8433 (ttmt) REVERT: A 614 ASP cc_start: 0.8697 (t0) cc_final: 0.8445 (t0) REVERT: A 683 ARG cc_start: 0.7565 (ptm160) cc_final: 0.7128 (ptt90) REVERT: A 714 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7427 (mpp-170) REVERT: C 92 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5631 (tp-100) REVERT: C 93 ASP cc_start: 0.5696 (t0) cc_final: 0.5399 (t0) REVERT: C 100 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: C 200 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6154 (tttm) REVERT: C 302 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7266 (tttp) REVERT: C 308 ARG cc_start: 0.6716 (tpm-80) cc_final: 0.6410 (tpp-160) REVERT: C 378 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6514 (ttt) REVERT: C 504 MET cc_start: 0.6720 (tpp) cc_final: 0.6374 (mpp) REVERT: C 736 ASN cc_start: 0.6385 (m110) cc_final: 0.5998 (m110) REVERT: C 787 GLU cc_start: 0.2022 (OUTLIER) cc_final: 0.0619 (tp30) REVERT: B 149 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5562 (mmm) REVERT: B 166 MET cc_start: 0.3413 (tpp) cc_final: 0.2893 (tmm) REVERT: B 206 LEU cc_start: 0.5273 (mt) cc_final: 0.5050 (mp) REVERT: B 252 PHE cc_start: 0.6568 (m-80) cc_final: 0.6203 (m-80) REVERT: B 256 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.5771 (tmt) REVERT: B 611 LYS cc_start: 0.7763 (ttpp) cc_final: 0.6584 (tttm) REVERT: B 615 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5727 (mp0) outliers start: 61 outliers final: 29 residues processed: 233 average time/residue: 0.6867 time to fit residues: 176.8512 Evaluate side-chains 212 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 198 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.194841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144321 restraints weight = 18948.298| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.25 r_work: 0.3557 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17224 Z= 0.157 Angle : 0.648 9.239 23358 Z= 0.335 Chirality : 0.046 0.193 2478 Planarity : 0.005 0.057 3024 Dihedral : 9.747 102.665 2406 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.90 % Favored : 90.90 % Rotamer: Outliers : 3.64 % Allowed : 27.20 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 2056 helix: 0.32 (0.25), residues: 443 sheet: -0.19 (0.24), residues: 425 loop : -1.68 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.019 0.002 TYR B 233 PHE 0.024 0.002 PHE B 651 TRP 0.022 0.002 TRP A 445 HIS 0.005 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00357 (17218) covalent geometry : angle 0.64327 (23340) hydrogen bonds : bond 0.04930 ( 491) hydrogen bonds : angle 5.31526 ( 1377) link_ALPHA1-4 : bond 0.01510 ( 6) link_ALPHA1-4 : angle 2.85636 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4458 (t70) REVERT: A 135 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: A 187 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8052 (tmt-80) REVERT: A 358 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: A 611 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8473 (ttmt) REVERT: A 614 ASP cc_start: 0.8750 (t0) cc_final: 0.8504 (t0) REVERT: A 678 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7430 (t0) REVERT: A 683 ARG cc_start: 0.7614 (ptm160) cc_final: 0.7123 (ptt90) REVERT: A 705 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 714 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7433 (mpp-170) REVERT: C 92 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5656 (tp-100) REVERT: C 93 ASP cc_start: 0.5540 (t0) cc_final: 0.5162 (t0) REVERT: C 100 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: C 139 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.5143 (p0) REVERT: C 200 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6135 (tttm) REVERT: C 302 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7231 (tttp) REVERT: C 308 ARG cc_start: 0.6748 (tpm-80) cc_final: 0.6484 (tpp-160) REVERT: C 378 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6604 (ttt) REVERT: C 635 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5661 (pp) REVERT: C 787 GLU cc_start: 0.2093 (OUTLIER) cc_final: 0.0710 (tp30) REVERT: B 149 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.4740 (ttm) REVERT: B 166 MET cc_start: 0.3233 (tpp) cc_final: 0.2770 (tmm) REVERT: B 206 LEU cc_start: 0.5260 (mt) cc_final: 0.5051 (mp) REVERT: B 252 PHE cc_start: 0.6585 (m-80) cc_final: 0.6200 (m-80) REVERT: B 256 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.5828 (tmt) REVERT: B 595 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6706 (tptp) REVERT: B 611 LYS cc_start: 0.7746 (ttpp) cc_final: 0.6553 (tttm) REVERT: B 615 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5817 (mp0) outliers start: 67 outliers final: 40 residues processed: 227 average time/residue: 0.6775 time to fit residues: 170.3714 Evaluate side-chains 225 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 0.0170 chunk 21 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 678 ASN C 161 HIS ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142960 restraints weight = 18941.714| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.00 r_work: 0.3553 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17224 Z= 0.185 Angle : 0.689 8.947 23358 Z= 0.359 Chirality : 0.048 0.206 2478 Planarity : 0.005 0.058 3024 Dihedral : 9.886 101.812 2406 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.05 % Favored : 90.76 % Rotamer: Outliers : 3.75 % Allowed : 27.09 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2056 helix: 0.19 (0.25), residues: 440 sheet: -0.30 (0.24), residues: 432 loop : -1.73 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 416 TYR 0.019 0.002 TYR B 581 PHE 0.026 0.002 PHE B 651 TRP 0.036 0.002 TRP A 445 HIS 0.006 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00426 (17218) covalent geometry : angle 0.68425 (23340) hydrogen bonds : bond 0.05517 ( 491) hydrogen bonds : angle 5.48260 ( 1377) link_ALPHA1-4 : bond 0.01457 ( 6) link_ALPHA1-4 : angle 2.87458 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: A 187 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8043 (tmt-80) REVERT: A 358 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: A 611 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8493 (ttmt) REVERT: A 614 ASP cc_start: 0.8697 (t0) cc_final: 0.8459 (t0) REVERT: A 683 ARG cc_start: 0.7685 (ptm160) cc_final: 0.7196 (ptt90) REVERT: A 705 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 710 MET cc_start: 0.8617 (mtt) cc_final: 0.8320 (mtt) REVERT: A 714 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7398 (mpp-170) REVERT: C 92 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.5878 (tp-100) REVERT: C 93 ASP cc_start: 0.5524 (t0) cc_final: 0.5205 (t0) REVERT: C 100 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: C 139 ASP cc_start: 0.5522 (OUTLIER) cc_final: 0.5087 (p0) REVERT: C 200 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6165 (tttm) REVERT: C 284 ASP cc_start: 0.8109 (t70) cc_final: 0.7374 (t0) REVERT: C 302 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7268 (tttp) REVERT: C 308 ARG cc_start: 0.6696 (tpm-80) cc_final: 0.6422 (tpp-160) REVERT: C 378 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6644 (ttt) REVERT: C 571 LEU cc_start: 0.5063 (OUTLIER) cc_final: 0.4629 (mp) REVERT: C 787 GLU cc_start: 0.2049 (OUTLIER) cc_final: 0.0597 (tp30) REVERT: B 149 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.4664 (ttm) REVERT: B 166 MET cc_start: 0.3327 (tpp) cc_final: 0.2838 (tmm) REVERT: B 206 LEU cc_start: 0.5320 (mt) cc_final: 0.5097 (mp) REVERT: B 252 PHE cc_start: 0.6680 (m-80) cc_final: 0.6310 (m-80) REVERT: B 595 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6862 (tptp) REVERT: B 611 LYS cc_start: 0.7688 (ttpp) cc_final: 0.6508 (tttm) REVERT: B 615 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5828 (mp0) outliers start: 69 outliers final: 40 residues processed: 227 average time/residue: 0.6600 time to fit residues: 166.0296 Evaluate side-chains 226 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 595 LYS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 162 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150572 restraints weight = 18937.007| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.26 r_work: 0.3586 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17224 Z= 0.115 Angle : 0.598 8.617 23358 Z= 0.308 Chirality : 0.044 0.173 2478 Planarity : 0.004 0.054 3024 Dihedral : 9.462 102.433 2405 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.88 % Favored : 91.93 % Rotamer: Outliers : 3.42 % Allowed : 27.52 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2056 helix: 0.45 (0.26), residues: 438 sheet: -0.17 (0.24), residues: 426 loop : -1.65 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.021 0.001 TYR B 233 PHE 0.019 0.001 PHE B 651 TRP 0.029 0.001 TRP A 445 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00254 (17218) covalent geometry : angle 0.59285 (23340) hydrogen bonds : bond 0.03723 ( 491) hydrogen bonds : angle 5.17920 ( 1377) link_ALPHA1-4 : bond 0.01574 ( 6) link_ALPHA1-4 : angle 2.81394 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8242.65 seconds wall clock time: 140 minutes 34.29 seconds (8434.29 seconds total)