Starting phenix.real_space_refine on Tue Jul 29 04:24:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h94_34554/07_2025/8h94_34554.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h94_34554/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h94_34554/07_2025/8h94_34554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h94_34554/07_2025/8h94_34554.map" model { file = "/net/cci-nas-00/data/ceres_data/8h94_34554/07_2025/8h94_34554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h94_34554/07_2025/8h94_34554.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS: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: 6.62, per 1000 atoms: 0.60 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.46 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: 4.29 Time building geometry restraints manager: 2.95 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:42.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.970 ------------------------------------------------------------------------------- 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 : 9.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.002 TRP A 184 HIS 0.005 0.001 HIS A 367 PHE 0.017 0.002 PHE B 157 TYR 0.013 0.001 TYR A 101 ARG 0.008 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.16234 ( 443) hydrogen bonds : angle 6.23186 ( 1278) covalent geometry : bond 0.00469 (11313) covalent geometry : angle 0.73677 (15322) *********************** 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 : 1.229 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: 1.4505 time to fit residues: 273.0570 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 : 1.162 ------------------------------------------------------------------------------- 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 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 532 ASN B 547 GLN C 98 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110988 restraints weight = 14198.910| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.55 r_work: 0.3196 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11313 Z= 0.165 Angle : 0.604 7.479 15322 Z= 0.310 Chirality : 0.043 0.147 1764 Planarity : 0.004 0.039 1939 Dihedral : 5.882 53.191 1514 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.84 % Allowed : 22.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1395 helix: 1.50 (0.23), residues: 524 sheet: -0.38 (0.32), residues: 301 loop : -1.66 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 184 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE A 693 TYR 0.011 0.001 TYR A 101 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 443) hydrogen bonds : angle 4.46162 ( 1278) covalent geometry : bond 0.00389 (11313) covalent geometry : angle 0.60432 (15322) *********************** 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 238 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 165 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 204 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6869 (mm) REVERT: A 213 GLU cc_start: 0.7442 (tp30) cc_final: 0.7136 (pt0) REVERT: A 310 ARG cc_start: 0.6525 (ttm170) cc_final: 0.6150 (mtt180) REVERT: A 408 ASP cc_start: 0.7558 (t70) cc_final: 0.7290 (p0) REVERT: A 555 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: A 647 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 841 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (tm) REVERT: A 900 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: B 329 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8495 (ttm-80) REVERT: B 507 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6275 (m-30) REVERT: C 40 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: C 66 SER cc_start: 0.8398 (t) cc_final: 0.8038 (m) outliers start: 73 outliers final: 29 residues processed: 219 average time/residue: 1.2373 time to fit residues: 293.5605 Evaluate side-chains 184 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 275 LYS 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 771 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU 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 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 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 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 84 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 78 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109062 restraints weight = 14483.314| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.49 r_work: 0.3158 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11313 Z= 0.177 Angle : 0.602 7.108 15322 Z= 0.309 Chirality : 0.043 0.147 1764 Planarity : 0.004 0.041 1939 Dihedral : 5.842 51.068 1502 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.28 % Allowed : 23.84 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1395 helix: 1.64 (0.23), residues: 524 sheet: -0.41 (0.32), residues: 300 loop : -1.70 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 PHE 0.012 0.001 PHE A 693 TYR 0.024 0.002 TYR A 247 ARG 0.006 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 443) hydrogen bonds : angle 4.30258 ( 1278) covalent geometry : bond 0.00420 (11313) covalent geometry : angle 0.60184 (15322) *********************** 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 228 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 310 ARG cc_start: 0.6677 (ttm170) cc_final: 0.6177 (mtt180) REVERT: A 408 ASP cc_start: 0.7530 (t70) cc_final: 0.7056 (t0) REVERT: A 555 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 643 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7465 (ptpp) REVERT: A 647 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8193 (mm) REVERT: A 680 GLU cc_start: 0.8068 (mp0) cc_final: 0.7860 (mt-10) REVERT: A 709 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7416 (mtmt) REVERT: A 799 CYS cc_start: 0.8204 (m) cc_final: 0.7994 (t) REVERT: A 841 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8308 (tm) REVERT: A 851 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 900 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: A 910 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: A 914 GLU cc_start: 0.6995 (pm20) cc_final: 0.6716 (mm-30) REVERT: A 921 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7878 (p) REVERT: B 329 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8475 (ttm-80) REVERT: B 507 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6173 (m-30) REVERT: C 40 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: C 66 SER cc_start: 0.8480 (t) cc_final: 0.8117 (m) outliers start: 66 outliers final: 34 residues processed: 211 average time/residue: 1.1511 time to fit residues: 263.6223 Evaluate side-chains 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 LEU 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 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 627 GLU 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 754 ARG Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 ILE 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 900 GLU Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 974 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107690 restraints weight = 14408.334| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.68 r_work: 0.3172 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11313 Z= 0.182 Angle : 0.599 7.395 15322 Z= 0.308 Chirality : 0.043 0.145 1764 Planarity : 0.004 0.041 1939 Dihedral : 5.914 59.203 1500 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 6.24 % Allowed : 23.12 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1395 helix: 1.65 (0.22), residues: 527 sheet: -0.45 (0.32), residues: 299 loop : -1.71 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 PHE 0.012 0.001 PHE A 676 TYR 0.021 0.002 TYR A 247 ARG 0.006 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 443) hydrogen bonds : angle 4.22225 ( 1278) covalent geometry : bond 0.00432 (11313) covalent geometry : angle 0.59914 (15322) *********************** 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 234 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 156 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 246 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7576 (mt) REVERT: A 310 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6114 (mtt180) REVERT: A 408 ASP cc_start: 0.7579 (t70) cc_final: 0.7093 (t0) REVERT: A 555 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 643 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7463 (ptpp) REVERT: A 647 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 709 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7430 (mtmt) REVERT: A 724 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7229 (tmtp) REVERT: A 841 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8364 (tm) REVERT: A 851 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 900 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: A 910 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: B 329 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7721 (mtp-110) REVERT: B 345 TYR cc_start: 0.8664 (m-10) cc_final: 0.8171 (m-10) REVERT: B 347 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6519 (mpp-170) REVERT: B 387 GLU cc_start: 0.7267 (pm20) cc_final: 0.7057 (pm20) REVERT: C 40 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8650 (mp0) REVERT: C 66 SER cc_start: 0.8510 (t) cc_final: 0.8178 (m) outliers start: 78 outliers final: 40 residues processed: 212 average time/residue: 1.4358 time to fit residues: 328.5872 Evaluate side-chains 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 310 ARG 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 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 627 GLU Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 865 ASN Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 974 SER 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 347 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 418 THR 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 511 ASN 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 76 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.144177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110741 restraints weight = 14286.391| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.58 r_work: 0.3199 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1818 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= 0.112 Angle : 0.539 7.216 15322 Z= 0.276 Chirality : 0.040 0.135 1764 Planarity : 0.003 0.042 1939 Dihedral : 5.529 50.852 1500 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.28 % Allowed : 23.52 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1395 helix: 1.95 (0.23), residues: 522 sheet: -0.35 (0.33), residues: 293 loop : -1.69 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 184 HIS 0.003 0.001 HIS A 315 PHE 0.009 0.001 PHE A 693 TYR 0.024 0.001 TYR A 247 ARG 0.007 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 443) hydrogen bonds : angle 3.94697 ( 1278) covalent geometry : bond 0.00258 (11313) covalent geometry : angle 0.53867 (15322) *********************** 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 228 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 408 ASP cc_start: 0.7780 (t70) cc_final: 0.7373 (t0) REVERT: A 489 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 555 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: A 647 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 680 GLU cc_start: 0.8244 (mp0) cc_final: 0.8026 (mt-10) REVERT: A 709 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7299 (mtmt) REVERT: A 724 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7220 (tmtp) REVERT: A 955 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8755 (tm) REVERT: B 329 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (ttm-80) REVERT: B 468 GLN cc_start: 0.8062 (pm20) cc_final: 0.7304 (mm-40) REVERT: B 532 ASN cc_start: 0.7475 (m-40) cc_final: 0.7260 (m110) REVERT: C 66 SER cc_start: 0.8518 (t) cc_final: 0.8180 (m) outliers start: 66 outliers final: 30 residues processed: 210 average time/residue: 1.1760 time to fit residues: 268.5096 Evaluate side-chains 193 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 246 ILE 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 429 LEU 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 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 772 SER 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 955 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 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 511 ASN 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 124 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.0040 chunk 95 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108312 restraints weight = 14415.311| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.55 r_work: 0.3159 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1862 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= 0.171 Angle : 0.595 8.662 15322 Z= 0.303 Chirality : 0.043 0.141 1764 Planarity : 0.004 0.042 1939 Dihedral : 5.580 50.925 1498 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.20 % Allowed : 24.88 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1395 helix: 1.81 (0.23), residues: 525 sheet: -0.27 (0.34), residues: 274 loop : -1.78 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 PHE 0.012 0.001 PHE A 676 TYR 0.023 0.001 TYR A 247 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 443) hydrogen bonds : angle 4.13101 ( 1278) covalent geometry : bond 0.00405 (11313) covalent geometry : angle 0.59465 (15322) *********************** 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 213 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 310 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6198 (mtt180) REVERT: A 408 ASP cc_start: 0.7718 (t70) cc_final: 0.7301 (t0) REVERT: A 555 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: A 647 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 709 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7444 (mtmt) REVERT: A 724 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7237 (tmtp) REVERT: A 841 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8490 (tm) REVERT: B 148 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6350 (tp40) REVERT: B 329 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7788 (mtp-110) REVERT: B 468 GLN cc_start: 0.8128 (pm20) cc_final: 0.7430 (mm-40) REVERT: C 58 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6288 (mp) REVERT: C 66 SER cc_start: 0.8487 (t) cc_final: 0.8129 (m) outliers start: 65 outliers final: 37 residues processed: 196 average time/residue: 1.4672 time to fit residues: 316.1307 Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 182 ILE 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 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 706 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU 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 A residue 974 SER 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 329 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 511 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 267 GLN B 532 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106759 restraints weight = 14527.656| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.55 r_work: 0.3142 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11313 Z= 0.203 Angle : 0.627 9.215 15322 Z= 0.319 Chirality : 0.044 0.142 1764 Planarity : 0.004 0.041 1939 Dihedral : 5.615 51.688 1496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.52 % Allowed : 24.96 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1395 helix: 1.68 (0.22), residues: 525 sheet: -0.34 (0.33), residues: 290 loop : -1.76 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 PHE 0.014 0.002 PHE A 676 TYR 0.019 0.002 TYR A 247 ARG 0.007 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 443) hydrogen bonds : angle 4.27399 ( 1278) covalent geometry : bond 0.00484 (11313) covalent geometry : angle 0.62688 (15322) *********************** 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 216 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 147 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 310 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6227 (mtt180) REVERT: A 408 ASP cc_start: 0.7586 (t70) cc_final: 0.7193 (t0) REVERT: A 555 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: A 647 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 709 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7536 (mtmt) REVERT: A 724 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7375 (tmtp) REVERT: A 841 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8434 (tm) REVERT: A 851 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 955 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8904 (tm) REVERT: B 148 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6558 (tp40) REVERT: B 329 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7644 (mtp-110) REVERT: B 468 GLN cc_start: 0.8013 (pm20) cc_final: 0.7504 (mm-40) REVERT: C 58 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6299 (mp) REVERT: C 66 SER cc_start: 0.8472 (t) cc_final: 0.8099 (m) outliers start: 69 outliers final: 38 residues processed: 199 average time/residue: 1.0893 time to fit residues: 235.7688 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 182 ILE 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 351 THR 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 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 627 GLU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 ILE 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 955 LEU Chi-restraints excluded: chain A residue 974 SER 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 329 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 473 SER 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 506 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 0.0870 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.2040 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108958 restraints weight = 14418.393| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.45 r_work: 0.3181 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11313 Z= 0.161 Angle : 0.595 9.288 15322 Z= 0.304 Chirality : 0.042 0.137 1764 Planarity : 0.004 0.041 1939 Dihedral : 5.476 58.528 1496 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.80 % Allowed : 25.84 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1395 helix: 1.74 (0.22), residues: 529 sheet: -0.38 (0.33), residues: 291 loop : -1.72 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 184 HIS 0.003 0.001 HIS A 104 PHE 0.011 0.001 PHE A 676 TYR 0.019 0.001 TYR A 247 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 443) hydrogen bonds : angle 4.15575 ( 1278) covalent geometry : bond 0.00384 (11313) covalent geometry : angle 0.59475 (15322) *********************** 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: A 310 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6333 (ttm170) REVERT: A 408 ASP cc_start: 0.7589 (t70) cc_final: 0.7189 (t0) REVERT: A 555 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 647 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 709 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7480 (mtmt) REVERT: A 724 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7344 (tmtp) REVERT: A 841 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8405 (tm) REVERT: A 851 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 955 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8839 (tm) REVERT: B 148 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6592 (tp40) REVERT: B 329 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8510 (ttm-80) REVERT: B 468 GLN cc_start: 0.7991 (pm20) cc_final: 0.7493 (mm-40) REVERT: C 58 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6329 (mp) outliers start: 60 outliers final: 39 residues processed: 191 average time/residue: 1.1522 time to fit residues: 239.1068 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 351 THR 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 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 706 THR 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 772 SER Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 ILE 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 974 SER 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 329 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 473 SER 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 511 ASN Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.140479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105577 restraints weight = 14459.665| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.76 r_work: 0.3147 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11313 Z= 0.174 Angle : 0.615 9.728 15322 Z= 0.315 Chirality : 0.042 0.140 1764 Planarity : 0.004 0.042 1939 Dihedral : 5.403 51.464 1496 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.12 % Allowed : 25.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1395 helix: 1.76 (0.22), residues: 521 sheet: -0.39 (0.32), residues: 291 loop : -1.68 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 184 HIS 0.004 0.001 HIS A 104 PHE 0.026 0.001 PHE A 833 TYR 0.022 0.002 TYR A 247 ARG 0.007 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 443) hydrogen bonds : angle 4.20966 ( 1278) covalent geometry : bond 0.00415 (11313) covalent geometry : angle 0.61532 (15322) *********************** 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.6877 (m-80) cc_final: 0.6655 (m-80) REVERT: A 204 LEU cc_start: 0.7743 (mm) cc_final: 0.7455 (pp) REVERT: A 307 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: A 310 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6277 (ttm170) REVERT: A 388 VAL cc_start: 0.8857 (t) cc_final: 0.8531 (m) REVERT: A 408 ASP cc_start: 0.7614 (t70) cc_final: 0.7196 (t0) REVERT: A 555 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 647 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 709 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7609 (mtmt) REVERT: A 724 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7248 (tmtp) REVERT: A 841 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (tm) REVERT: A 955 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8826 (tm) REVERT: B 148 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6531 (tp40) REVERT: B 329 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8432 (ttm-80) REVERT: B 429 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 468 GLN cc_start: 0.7980 (pm20) cc_final: 0.7475 (mm-40) REVERT: C 58 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6298 (mp) outliers start: 64 outliers final: 41 residues processed: 191 average time/residue: 1.1393 time to fit residues: 237.2780 Evaluate side-chains 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 351 THR 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 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 706 THR Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 841 LEU 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 974 SER 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 329 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 473 SER 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 506 VAL Chi-restraints excluded: chain B residue 511 ASN Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 575 SER 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 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.142347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107488 restraints weight = 14306.682| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.73 r_work: 0.3174 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2250 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= 0.129 Angle : 0.578 9.684 15322 Z= 0.294 Chirality : 0.041 0.179 1764 Planarity : 0.003 0.041 1939 Dihedral : 5.110 51.155 1496 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.40 % Allowed : 26.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1395 helix: 1.87 (0.23), residues: 522 sheet: -0.37 (0.33), residues: 285 loop : -1.67 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 184 HIS 0.003 0.001 HIS A 315 PHE 0.025 0.001 PHE A 833 TYR 0.022 0.001 TYR A 247 ARG 0.008 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 443) hydrogen bonds : angle 4.05076 ( 1278) covalent geometry : bond 0.00303 (11313) covalent geometry : angle 0.57794 (15322) ********************** 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 205 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6316 (ptp-110) cc_final: 0.6028 (ptm160) REVERT: A 307 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: A 310 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6322 (ttm170) REVERT: A 388 VAL cc_start: 0.8772 (t) cc_final: 0.8435 (m) REVERT: A 408 ASP cc_start: 0.7527 (t70) cc_final: 0.7136 (t0) REVERT: A 555 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 647 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 709 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7471 (mtmt) REVERT: A 724 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7179 (tmtp) REVERT: A 955 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8699 (tm) REVERT: B 148 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6639 (tp40) REVERT: B 175 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.6022 (tp40) REVERT: B 329 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (ttm-80) REVERT: B 468 GLN cc_start: 0.7820 (pm20) cc_final: 0.7414 (mm-40) REVERT: C 58 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6210 (mp) outliers start: 55 outliers final: 37 residues processed: 190 average time/residue: 1.1089 time to fit residues: 230.0649 Evaluate side-chains 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 351 THR 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 555 GLU 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 772 SER Chi-restraints excluded: chain A residue 800 HIS 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 974 SER 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 329 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 473 SER 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 506 VAL Chi-restraints excluded: chain B residue 511 ASN Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 575 SER 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 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 0.0370 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107583 restraints weight = 14355.268| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.76 r_work: 0.3194 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 11313 Z= 0.173 Angle : 0.850 59.177 15322 Z= 0.478 Chirality : 0.042 0.431 1764 Planarity : 0.003 0.042 1939 Dihedral : 5.071 51.188 1494 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.08 % Allowed : 26.72 % Favored : 69.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1395 helix: 1.88 (0.23), residues: 522 sheet: -0.36 (0.33), residues: 285 loop : -1.67 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 184 HIS 0.003 0.001 HIS A 315 PHE 0.023 0.001 PHE A 833 TYR 0.021 0.001 TYR A 247 ARG 0.007 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 443) hydrogen bonds : angle 4.05154 ( 1278) covalent geometry : bond 0.00400 (11313) covalent geometry : angle 0.85014 (15322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8823.84 seconds wall clock time: 154 minutes 8.11 seconds (9248.11 seconds total)