Starting phenix.real_space_refine on Sat Aug 23 08:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h94_34554/08_2025/8h94_34554.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.147 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 7057 2.51 5 N 1898 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7481 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 2.64, per 1000 atoms: 0.24 Number of scatterers: 11098 At special positions: 0 Unit cell: (89.134, 103.265, 130.44, 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 2052 8.00 N 1898 7.00 C 7057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 549.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 40.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.512A pdb=" N TYR A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.000A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.403A pdb=" N VAL A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.719A pdb=" N ASP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A 227 " --> pdb=" O ASP A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.511A pdb=" N VAL A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.702A pdb=" N GLN A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 356 through 373 removed outlier: 3.836A pdb=" N LYS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.519A pdb=" N GLN A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.908A pdb=" N GLN A 466 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 518 through 532 removed outlier: 4.047A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.755A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.511A pdb=" N LEU A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 684 through 693 removed outlier: 3.789A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.670A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 removed outlier: 3.671A pdb=" N ASN A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.998A pdb=" N GLY A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 removed outlier: 3.685A pdb=" N LEU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 938 through 949 removed outlier: 3.906A pdb=" N GLY A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 979 removed outlier: 3.518A pdb=" N CYS A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.744A pdb=" N GLU A1021 " --> pdb=" O TRP A1018 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1022' Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.581A pdb=" N SER A1049 " --> pdb=" O TRP A1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 174 removed outlier: 3.506A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 171 " --> pdb=" O TRP B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.606A pdb=" N GLU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 41' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.950A pdb=" N ARG C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.415A pdb=" N PHE A 217 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR A 267 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 219 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 140 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 286 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 142 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL A 288 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS A 144 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432 Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 571 removed outlier: 6.913A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 701 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 730 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 758 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 787 " --> pdb=" O CYS A 816 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 815 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 844 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 872 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 901 " --> pdb=" O ASP A 930 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 986 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.517A pdb=" N ALA B 283 " --> pdb=" O LYS B 580 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 576 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 289 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA B 574 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 556 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.542A pdb=" N VAL B 298 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 351 removed outlier: 6.828A pdb=" N GLY B 361 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 349 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 359 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU B 351 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 357 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 370 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 372 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR B 379 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 396 removed outlier: 6.546A pdb=" N VAL B 411 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN B 424 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 413 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 420 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 437 removed outlier: 6.501A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 476 removed outlier: 6.578A pdb=" N GLY B 486 " --> pdb=" O MET B 472 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 474 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS B 476 " --> pdb=" O TRP B 482 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TRP B 482 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 6.637A pdb=" N VAL B 528 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 516 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 526 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE B 518 " --> pdb=" O TRP B 524 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP B 524 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 443 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3170 1.33 - 1.45: 1851 1.45 - 1.58: 6164 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 11313 Sorted by residual: bond pdb=" CA SER A 653 " pdb=" CB SER A 653 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.61e-02 3.86e+03 8.38e+00 bond pdb=" CA LEU A 498 " pdb=" C LEU A 498 " ideal model delta sigma weight residual 1.522 1.481 0.040 1.43e-02 4.89e+03 8.00e+00 bond pdb=" N LEU A 645 " pdb=" CA LEU A 645 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.45e+00 bond pdb=" N HIS A 116 " pdb=" CA HIS A 116 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.50e+00 bond pdb=" N ASP A 649 " pdb=" CA ASP A 649 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.26e-02 6.30e+03 6.48e+00 ... (remaining 11308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 14914 2.02 - 4.04: 347 4.04 - 6.06: 51 6.06 - 8.08: 9 8.08 - 10.10: 1 Bond angle restraints: 15322 Sorted by residual: angle pdb=" N VAL C 41 " pdb=" CA VAL C 41 " pdb=" C VAL C 41 " ideal model delta sigma weight residual 112.83 108.52 4.31 9.90e-01 1.02e+00 1.89e+01 angle pdb=" N MET A 499 " pdb=" CA MET A 499 " pdb=" C MET A 499 " ideal model delta sigma weight residual 113.15 117.88 -4.73 1.19e+00 7.06e-01 1.58e+01 angle pdb=" CA PRO B 540 " pdb=" N PRO B 540 " pdb=" CD PRO B 540 " ideal model delta sigma weight residual 112.00 106.54 5.46 1.40e+00 5.10e-01 1.52e+01 angle pdb=" N LEU A 647 " pdb=" CA LEU A 647 " pdb=" C LEU A 647 " ideal model delta sigma weight residual 113.16 108.54 4.62 1.24e+00 6.50e-01 1.39e+01 angle pdb=" N PRO A 120 " pdb=" CA PRO A 120 " pdb=" C PRO A 120 " ideal model delta sigma weight residual 113.53 108.38 5.15 1.39e+00 5.18e-01 1.37e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5758 17.10 - 34.19: 794 34.19 - 51.29: 235 51.29 - 68.39: 41 68.39 - 85.48: 21 Dihedral angle restraints: 6849 sinusoidal: 2750 harmonic: 4099 Sorted by residual: dihedral pdb=" CA MET B 458 " pdb=" C MET B 458 " pdb=" N ALA B 459 " pdb=" CA ALA B 459 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 291 " pdb=" C LYS B 291 " pdb=" N HIS B 292 " pdb=" CA HIS B 292 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU A 846 " pdb=" C LEU A 846 " pdb=" N ASN A 847 " pdb=" CA ASN A 847 " ideal model delta harmonic sigma weight residual 180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1525 0.066 - 0.131: 221 0.131 - 0.197: 16 0.197 - 0.262: 0 0.262 - 0.328: 2 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ILE A 651 " pdb=" N ILE A 651 " pdb=" C ILE A 651 " pdb=" CB ILE A 651 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA LEU A 498 " pdb=" N LEU A 498 " pdb=" C LEU A 498 " pdb=" CB LEU A 498 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET A 499 " pdb=" N MET A 499 " pdb=" C MET A 499 " pdb=" CB MET A 499 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 1761 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 539 " 0.055 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO B 540 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 540 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 540 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 114 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C ASP A 114 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP A 114 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 115 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 184 " 0.017 2.00e-02 2.50e+03 1.34e-02 4.50e+00 pdb=" CG TRP A 184 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 184 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 184 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 184 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 184 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 184 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 184 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 184 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 184 " 0.002 2.00e-02 2.50e+03 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 206 2.68 - 3.24: 10276 3.24 - 3.79: 16509 3.79 - 4.35: 22284 4.35 - 4.90: 37827 Nonbonded interactions: 87102 Sorted by model distance: nonbonded pdb=" NH2 ARG A 402 " pdb=" OD2 ASP A 409 " model vdw 2.127 3.120 nonbonded pdb=" OH TYR A 101 " pdb=" OE2 GLU A 197 " model vdw 2.195 3.040 nonbonded pdb=" N GLU A1051 " pdb=" OE1 GLU A1051 " model vdw 2.195 3.120 nonbonded pdb=" N GLN B 468 " pdb=" OE1 GLN B 468 " model vdw 2.200 3.120 nonbonded pdb=" N GLN A 381 " pdb=" OE1 GLN A 381 " model vdw 2.227 3.120 ... (remaining 87097 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: 0.540 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11313 Z= 0.226 Angle : 0.737 10.103 15322 Z= 0.409 Chirality : 0.046 0.328 1764 Planarity : 0.004 0.082 1939 Dihedral : 17.624 85.483 4177 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.08 % Allowed : 28.48 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1395 helix: 1.14 (0.23), residues: 510 sheet: -0.52 (0.32), residues: 305 loop : -1.67 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 599 TYR 0.013 0.001 TYR A 101 PHE 0.017 0.002 PHE B 157 TRP 0.036 0.002 TRP A 184 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00469 (11313) covalent geometry : angle 0.73677 (15322) hydrogen bonds : bond 0.16234 ( 443) hydrogen bonds : angle 6.23186 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7283 (tp30) cc_final: 0.6927 (pp20) REVERT: A 247 TYR cc_start: 0.7314 (p90) cc_final: 0.7094 (p90) REVERT: A 643 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7886 (ptpp) REVERT: A 710 ASP cc_start: 0.7095 (t0) cc_final: 0.6891 (t0) outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.5544 time to fit residues: 104.1639 Evaluate side-chains 163 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 866 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 535 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A 832 GLN A 848 HIS A 910 GLN A 934 ASN A 950 GLN B 511 ASN B 532 ASN B 547 GLN C 98 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113257 restraints weight = 14266.561| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.56 r_work: 0.3205 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11313 Z= 0.122 Angle : 0.561 6.934 15322 Z= 0.287 Chirality : 0.041 0.142 1764 Planarity : 0.004 0.039 1939 Dihedral : 5.575 55.095 1514 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.76 % Allowed : 22.88 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.23), residues: 1395 helix: 1.63 (0.23), residues: 522 sheet: -0.41 (0.32), residues: 306 loop : -1.59 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 599 TYR 0.010 0.001 TYR A 101 PHE 0.011 0.001 PHE A 693 TRP 0.037 0.001 TRP A 184 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00279 (11313) covalent geometry : angle 0.56077 (15322) hydrogen bonds : bond 0.03715 ( 443) hydrogen bonds : angle 4.32972 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 164 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6711 (mm) REVERT: A 408 ASP cc_start: 0.7516 (t70) cc_final: 0.7276 (p0) REVERT: A 555 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 647 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 733 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7729 (p0) REVERT: A 900 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 347 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7664 (mpt180) REVERT: B 507 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6167 (m-30) REVERT: C 40 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8512 (mm-30) REVERT: C 69 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8183 (mt-10) outliers start: 72 outliers final: 28 residues processed: 216 average time/residue: 0.5271 time to fit residues: 123.5700 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 100 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN B 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111989 restraints weight = 14471.720| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.58 r_work: 0.3201 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11313 Z= 0.141 Angle : 0.572 7.700 15322 Z= 0.293 Chirality : 0.042 0.146 1764 Planarity : 0.003 0.040 1939 Dihedral : 5.435 50.621 1502 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.96 % Allowed : 23.44 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.23), residues: 1395 helix: 1.82 (0.23), residues: 521 sheet: -0.29 (0.33), residues: 286 loop : -1.70 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.025 0.001 TYR A 247 PHE 0.011 0.001 PHE A 693 TRP 0.030 0.001 TRP A 184 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00329 (11313) covalent geometry : angle 0.57233 (15322) hydrogen bonds : bond 0.03755 ( 443) hydrogen bonds : angle 4.15190 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6902 (mm) REVERT: A 213 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: A 408 ASP cc_start: 0.7553 (t70) cc_final: 0.7086 (t0) REVERT: A 555 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: A 647 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 709 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7253 (mtmt) REVERT: A 733 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 900 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 914 GLU cc_start: 0.7042 (pm20) cc_final: 0.6612 (mm-30) REVERT: A 921 THR cc_start: 0.8117 (m) cc_final: 0.7662 (p) REVERT: B 329 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (ttm-80) REVERT: B 507 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6259 (m-30) REVERT: B 532 ASN cc_start: 0.7430 (m-40) cc_final: 0.7228 (m110) REVERT: B 561 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 40 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: C 66 SER cc_start: 0.8392 (t) cc_final: 0.8059 (m) REVERT: C 69 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8423 (mt-10) outliers start: 62 outliers final: 33 residues processed: 207 average time/residue: 0.5454 time to fit residues: 121.9019 Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 133 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 6 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112114 restraints weight = 14422.171| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.80 r_work: 0.3219 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11313 Z= 0.112 Angle : 0.537 7.748 15322 Z= 0.273 Chirality : 0.040 0.154 1764 Planarity : 0.003 0.039 1939 Dihedral : 4.972 49.812 1498 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.72 % Allowed : 25.04 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.23), residues: 1395 helix: 1.96 (0.23), residues: 522 sheet: -0.32 (0.32), residues: 299 loop : -1.62 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.024 0.001 TYR A 247 PHE 0.009 0.001 PHE A 693 TRP 0.027 0.001 TRP A 184 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00257 (11313) covalent geometry : angle 0.53745 (15322) hydrogen bonds : bond 0.03157 ( 443) hydrogen bonds : angle 3.94834 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6203 (pm20) REVERT: A 246 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7463 (mt) REVERT: A 408 ASP cc_start: 0.7652 (t70) cc_final: 0.7187 (t0) REVERT: A 489 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 503 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8263 (mt) REVERT: A 555 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: A 647 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 914 GLU cc_start: 0.7135 (pm20) cc_final: 0.6737 (mm-30) REVERT: A 921 THR cc_start: 0.8236 (m) cc_final: 0.7768 (p) REVERT: B 148 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6258 (tp40) REVERT: B 448 ASP cc_start: 0.7393 (p0) cc_final: 0.6884 (t0) REVERT: B 539 MET cc_start: 0.7746 (tpt) cc_final: 0.7493 (tpt) REVERT: C 66 SER cc_start: 0.8469 (t) cc_final: 0.8148 (m) REVERT: C 69 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8414 (mt-10) REVERT: C 105 LEU cc_start: 0.8566 (mt) cc_final: 0.8300 (tt) outliers start: 59 outliers final: 30 residues processed: 205 average time/residue: 0.5189 time to fit residues: 115.6558 Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 865 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113774 restraints weight = 13915.747| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.74 r_work: 0.3228 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11313 Z= 0.169 Angle : 0.596 8.446 15322 Z= 0.303 Chirality : 0.043 0.147 1764 Planarity : 0.003 0.041 1939 Dihedral : 5.363 51.166 1498 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.00 % Allowed : 24.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.23), residues: 1395 helix: 1.90 (0.23), residues: 520 sheet: -0.37 (0.32), residues: 298 loop : -1.69 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.023 0.001 TYR A 247 PHE 0.012 0.001 PHE A 676 TRP 0.023 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00401 (11313) covalent geometry : angle 0.59626 (15322) hydrogen bonds : bond 0.03959 ( 443) hydrogen bonds : angle 4.13790 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6516 (pm20) REVERT: A 225 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: A 310 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6302 (mtt180) REVERT: A 408 ASP cc_start: 0.7678 (t70) cc_final: 0.7281 (t0) REVERT: A 503 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 555 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: A 647 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 709 LYS cc_start: 0.8027 (mppt) cc_final: 0.7664 (mtmt) REVERT: A 914 GLU cc_start: 0.7357 (pm20) cc_final: 0.7068 (mm-30) REVERT: A 955 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8884 (tm) REVERT: B 329 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7857 (mtp-110) REVERT: B 347 ARG cc_start: 0.8159 (tpp-160) cc_final: 0.7952 (mpt180) REVERT: C 66 SER cc_start: 0.8652 (t) cc_final: 0.8332 (m) REVERT: C 69 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8481 (mt-10) outliers start: 75 outliers final: 36 residues processed: 200 average time/residue: 0.5454 time to fit residues: 118.1471 Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 865 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN B 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117646 restraints weight = 13996.658| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.88 r_work: 0.3289 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11313 Z= 0.103 Angle : 0.533 8.321 15322 Z= 0.270 Chirality : 0.040 0.134 1764 Planarity : 0.003 0.044 1939 Dihedral : 4.953 49.963 1498 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.32 % Allowed : 25.68 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.23), residues: 1395 helix: 2.09 (0.23), residues: 522 sheet: -0.33 (0.33), residues: 294 loop : -1.62 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 295 TYR 0.023 0.001 TYR A 247 PHE 0.009 0.001 PHE A 693 TRP 0.019 0.001 TRP A 184 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00233 (11313) covalent geometry : angle 0.53282 (15322) hydrogen bonds : bond 0.02913 ( 443) hydrogen bonds : angle 3.85339 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: A 225 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (mtp) REVERT: A 310 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6270 (mtt180) REVERT: A 408 ASP cc_start: 0.7840 (t70) cc_final: 0.7457 (t0) REVERT: A 647 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8441 (mm) REVERT: A 709 LYS cc_start: 0.7930 (mppt) cc_final: 0.7551 (mtmt) REVERT: A 868 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7510 (ttpt) REVERT: A 876 MET cc_start: 0.9114 (mmm) cc_final: 0.8912 (mmt) REVERT: A 914 GLU cc_start: 0.7440 (pm20) cc_final: 0.7061 (mm-30) REVERT: A 955 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8698 (tm) REVERT: B 148 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6500 (tp40) REVERT: B 249 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8852 (mmtm) REVERT: B 448 ASP cc_start: 0.7503 (p0) cc_final: 0.7002 (t0) REVERT: B 468 GLN cc_start: 0.8014 (pm20) cc_final: 0.7269 (mm-40) REVERT: B 539 MET cc_start: 0.7684 (tpt) cc_final: 0.7447 (tpt) REVERT: C 40 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: C 58 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6233 (mp) REVERT: C 66 SER cc_start: 0.8617 (t) cc_final: 0.8308 (m) REVERT: C 69 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 105 LEU cc_start: 0.8610 (mt) cc_final: 0.8343 (tt) outliers start: 54 outliers final: 27 residues processed: 198 average time/residue: 0.5206 time to fit residues: 111.9358 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 865 ASN Chi-restraints excluded: chain A residue 868 LYS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 982 HIS B 511 ASN B 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112561 restraints weight = 14386.024| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.79 r_work: 0.3244 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11313 Z= 0.093 Angle : 0.523 8.997 15322 Z= 0.262 Chirality : 0.039 0.130 1764 Planarity : 0.003 0.046 1939 Dihedral : 4.631 48.644 1498 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.76 % Allowed : 26.40 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.23), residues: 1395 helix: 2.22 (0.23), residues: 522 sheet: -0.30 (0.32), residues: 299 loop : -1.57 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.020 0.001 TYR A 247 PHE 0.013 0.001 PHE A 858 TRP 0.020 0.001 TRP A 184 HIS 0.003 0.000 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00207 (11313) covalent geometry : angle 0.52299 (15322) hydrogen bonds : bond 0.02543 ( 443) hydrogen bonds : angle 3.71980 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: A 214 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.5283 (ptm160) REVERT: A 225 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7755 (mtp) REVERT: A 310 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.6139 (mtt180) REVERT: A 388 VAL cc_start: 0.8662 (t) cc_final: 0.8312 (m) REVERT: A 408 ASP cc_start: 0.7731 (t70) cc_final: 0.7302 (t0) REVERT: A 487 ARG cc_start: 0.7787 (ptt-90) cc_final: 0.7083 (ptp-110) REVERT: A 489 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 647 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 709 LYS cc_start: 0.7782 (mppt) cc_final: 0.7333 (mtmt) REVERT: A 876 MET cc_start: 0.8800 (mmm) cc_final: 0.8547 (mmt) REVERT: B 249 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8785 (mmtm) REVERT: B 448 ASP cc_start: 0.7195 (p0) cc_final: 0.6738 (t0) REVERT: B 468 GLN cc_start: 0.7885 (pm20) cc_final: 0.7170 (mm-40) REVERT: B 539 MET cc_start: 0.7567 (tpt) cc_final: 0.7310 (tpt) REVERT: C 40 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: C 58 ILE cc_start: 0.6494 (OUTLIER) cc_final: 0.6149 (mp) REVERT: C 66 SER cc_start: 0.8273 (t) cc_final: 0.7957 (m) REVERT: C 69 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8010 (mt-10) REVERT: C 105 LEU cc_start: 0.8492 (mt) cc_final: 0.8287 (tt) outliers start: 47 outliers final: 24 residues processed: 199 average time/residue: 0.4713 time to fit residues: 102.8978 Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN B 175 GLN B 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113685 restraints weight = 13956.959| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.36 r_work: 0.3212 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11313 Z= 0.255 Angle : 0.698 10.556 15322 Z= 0.353 Chirality : 0.046 0.149 1764 Planarity : 0.004 0.042 1939 Dihedral : 5.489 58.525 1494 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.48 % Allowed : 26.56 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.23), residues: 1395 helix: 1.69 (0.22), residues: 520 sheet: -0.31 (0.33), residues: 292 loop : -1.72 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.021 0.002 TYR A 247 PHE 0.017 0.002 PHE A 676 TRP 0.025 0.002 TRP A 184 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00610 (11313) covalent geometry : angle 0.69797 (15322) hydrogen bonds : bond 0.04644 ( 443) hydrogen bonds : angle 4.35679 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6115 (ptp-110) REVERT: A 408 ASP cc_start: 0.7569 (t70) cc_final: 0.7150 (t0) REVERT: A 643 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7819 (ptpp) REVERT: A 647 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 709 LYS cc_start: 0.8150 (mppt) cc_final: 0.7789 (mtmt) REVERT: B 468 GLN cc_start: 0.8090 (pm20) cc_final: 0.7467 (mm-40) REVERT: B 484 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 58 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6184 (mp) REVERT: C 66 SER cc_start: 0.8643 (t) cc_final: 0.8299 (m) outliers start: 56 outliers final: 27 residues processed: 182 average time/residue: 0.5402 time to fit residues: 106.6442 Evaluate side-chains 171 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.151255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116225 restraints weight = 13784.177| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.83 r_work: 0.3270 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11313 Z= 0.122 Angle : 0.592 10.434 15322 Z= 0.297 Chirality : 0.041 0.183 1764 Planarity : 0.003 0.041 1939 Dihedral : 5.019 56.237 1494 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.36 % Allowed : 27.84 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.23), residues: 1395 helix: 1.90 (0.23), residues: 521 sheet: -0.29 (0.33), residues: 286 loop : -1.65 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 295 TYR 0.021 0.001 TYR A 247 PHE 0.018 0.001 PHE A 858 TRP 0.021 0.001 TRP A 184 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00284 (11313) covalent geometry : angle 0.59186 (15322) hydrogen bonds : bond 0.03187 ( 443) hydrogen bonds : angle 3.99949 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 VAL cc_start: 0.8944 (t) cc_final: 0.8685 (m) REVERT: A 408 ASP cc_start: 0.7735 (t70) cc_final: 0.7362 (t0) REVERT: A 647 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8446 (mm) REVERT: A 709 LYS cc_start: 0.8023 (mppt) cc_final: 0.7680 (mtmt) REVERT: A 851 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 148 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6512 (tp40) REVERT: B 175 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6122 (tp40) REVERT: B 448 ASP cc_start: 0.7496 (p0) cc_final: 0.7048 (t0) REVERT: B 468 GLN cc_start: 0.7956 (pm20) cc_final: 0.7509 (mm-40) REVERT: C 40 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: C 58 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6248 (mp) REVERT: C 66 SER cc_start: 0.8559 (t) cc_final: 0.8246 (m) outliers start: 42 outliers final: 25 residues processed: 182 average time/residue: 0.4599 time to fit residues: 91.2595 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 130 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114172 restraints weight = 13959.937| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.65 r_work: 0.3233 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11313 Z= 0.180 Angle : 0.653 11.494 15322 Z= 0.326 Chirality : 0.043 0.182 1764 Planarity : 0.004 0.041 1939 Dihedral : 5.207 50.829 1494 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.04 % Allowed : 28.16 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.23), residues: 1395 helix: 1.63 (0.22), residues: 532 sheet: -0.29 (0.33), residues: 274 loop : -1.72 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 640 TYR 0.019 0.002 TYR A 247 PHE 0.017 0.002 PHE A 858 TRP 0.029 0.002 TRP B 167 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00429 (11313) covalent geometry : angle 0.65314 (15322) hydrogen bonds : bond 0.03970 ( 443) hydrogen bonds : angle 4.17752 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6389 (ptp-110) cc_final: 0.5910 (ptm160) REVERT: A 408 ASP cc_start: 0.7627 (t70) cc_final: 0.7269 (t0) REVERT: A 647 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 680 GLU cc_start: 0.8207 (mp0) cc_final: 0.7992 (mt-10) REVERT: A 709 LYS cc_start: 0.8085 (mppt) cc_final: 0.7751 (mtmt) REVERT: B 148 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6458 (tp40) REVERT: B 468 GLN cc_start: 0.7960 (pm20) cc_final: 0.7499 (mm-40) REVERT: C 40 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: C 58 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.6180 (mp) outliers start: 38 outliers final: 27 residues processed: 170 average time/residue: 0.4616 time to fit residues: 85.4846 Evaluate side-chains 173 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 6 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 511 ASN B 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111643 restraints weight = 14337.584| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.78 r_work: 0.3238 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11313 Z= 0.102 Angle : 0.568 10.625 15322 Z= 0.284 Chirality : 0.040 0.177 1764 Planarity : 0.003 0.042 1939 Dihedral : 4.716 50.126 1494 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.64 % Allowed : 28.40 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.23), residues: 1395 helix: 1.84 (0.23), residues: 534 sheet: -0.38 (0.32), residues: 294 loop : -1.56 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 754 TYR 0.020 0.001 TYR A 247 PHE 0.018 0.001 PHE A 858 TRP 0.022 0.001 TRP B 167 HIS 0.003 0.000 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00232 (11313) covalent geometry : angle 0.56827 (15322) hydrogen bonds : bond 0.02730 ( 443) hydrogen bonds : angle 3.85891 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.00 seconds wall clock time: 62 minutes 7.45 seconds (3727.45 seconds total)