Starting phenix.real_space_refine on Wed Sep 17 14:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6k_61175/09_2025/9j6k_61175.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 49 5.16 5 C 5667 2.51 5 N 1503 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8730 Classifications: {'peptide': 1115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1074} Chain breaks: 3 Chain: "B" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8936 At special positions: 0 Unit cell: (97.82, 101.17, 111.22, 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 49 16.00 O 1717 8.00 N 1503 7.00 C 5667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 246.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 25 sheets defined 7.3% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.831A pdb=" N ILE A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 254 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 3.633A pdb=" N TYR A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 removed outlier: 3.802A pdb=" N TRP A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1097 Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.862A pdb=" N VAL A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A1138 " --> pdb=" O GLU A1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.534A pdb=" N LEU B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 4.124A pdb=" N TYR A 3 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1028 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N SER A1027 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS A1009 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.682A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.619A pdb=" N LEU A 80 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 65 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 90 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 101 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.651A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.047A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 180 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 190 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 210 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.813A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 246 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 241 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.290A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 318 removed outlier: 3.591A pdb=" N THR A 315 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 332 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.823A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.823A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 402 through 405 removed outlier: 4.592A pdb=" N LEU A 404 " --> pdb=" O THR A 698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 411 through 413 removed outlier: 4.376A pdb=" N LEU A 425 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 444 " --> pdb=" O MET A 437 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 468 through 471 removed outlier: 7.235A pdb=" N VAL A 476 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU A 489 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 478 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 487 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 500 through 502 removed outlier: 3.890A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 508 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 519 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.737A pdb=" N ALA A 557 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 558 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 567 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 580 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 590 through 594 removed outlier: 4.273A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 605 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 602 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 614 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 640 removed outlier: 3.549A pdb=" N VAL A 637 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 639 " --> pdb=" O PHE A 650 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 660 through 661 Processing sheet with id=AC1, first strand: chain 'A' and resid 678 through 682 removed outlier: 3.557A pdb=" N LEU A 682 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 690 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.957A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 727 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS A 732 " --> pdb=" O GLN A 727 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 817 removed outlier: 5.164A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 872 through 875 removed outlier: 4.114A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 890 " --> pdb=" O CYS A 903 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N CYS A 903 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 911 through 917 removed outlier: 3.807A pdb=" N TYR A 913 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.335A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 975 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.335A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 975 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 636 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: 1.86 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 1453 1.46 - 1.58: 4674 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9099 Sorted by residual: bond pdb=" CA ILE A 848 " pdb=" CB ILE A 848 " ideal model delta sigma weight residual 1.531 1.547 -0.016 1.11e-02 8.12e+03 2.21e+00 bond pdb=" CA ARG A 419 " pdb=" CB ARG A 419 " ideal model delta sigma weight residual 1.526 1.545 -0.019 1.44e-02 4.82e+03 1.70e+00 bond pdb=" CG1 ILE A 178 " pdb=" CD1 ILE A 178 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CB ARG A 739 " pdb=" CG ARG A 739 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB VAL A 167 " pdb=" CG1 VAL A 167 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11494 1.76 - 3.53: 675 3.53 - 5.29: 121 5.29 - 7.06: 27 7.06 - 8.82: 7 Bond angle restraints: 12324 Sorted by residual: angle pdb=" N GLY A 609 " pdb=" CA GLY A 609 " pdb=" C GLY A 609 " ideal model delta sigma weight residual 114.37 109.29 5.08 1.26e+00 6.30e-01 1.63e+01 angle pdb=" CA ARG A 739 " pdb=" CB ARG A 739 " pdb=" CG ARG A 739 " ideal model delta sigma weight residual 114.10 106.77 7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" C ALA A 381 " pdb=" N PHE A 382 " pdb=" CA PHE A 382 " ideal model delta sigma weight residual 120.82 125.96 -5.14 1.50e+00 4.44e-01 1.18e+01 angle pdb=" N ILE A 587 " pdb=" CA ILE A 587 " pdb=" C ILE A 587 " ideal model delta sigma weight residual 108.95 112.25 -3.30 9.80e-01 1.04e+00 1.13e+01 angle pdb=" N GLU A 585 " pdb=" CA GLU A 585 " pdb=" C GLU A 585 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.07e+01 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5013 17.39 - 34.78: 423 34.78 - 52.16: 38 52.16 - 69.55: 4 69.55 - 86.94: 14 Dihedral angle restraints: 5492 sinusoidal: 2199 harmonic: 3293 Sorted by residual: dihedral pdb=" CA VAL A1108 " pdb=" C VAL A1108 " pdb=" N VAL A1109 " pdb=" CA VAL A1109 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLU A1107 " pdb=" C GLU A1107 " pdb=" N VAL A1108 " pdb=" CA VAL A1108 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ARG A 639 " pdb=" C ARG A 639 " pdb=" N THR A 640 " pdb=" CA THR A 640 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1035 0.052 - 0.105: 293 0.105 - 0.157: 83 0.157 - 0.210: 11 0.210 - 0.262: 2 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CB ILE A 848 " pdb=" CA ILE A 848 " pdb=" CG1 ILE A 848 " pdb=" CG2 ILE A 848 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE B 88 " pdb=" CA ILE B 88 " pdb=" CG1 ILE B 88 " pdb=" CG2 ILE B 88 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLU A1107 " pdb=" N GLU A1107 " pdb=" C GLU A1107 " pdb=" CB GLU A1107 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1421 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 739 " 0.049 9.50e-02 1.11e+02 3.17e-02 6.83e+00 pdb=" NE ARG A 739 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 739 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A 739 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 739 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 411 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 412 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 824 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 825 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 825 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 825 " -0.032 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 187 2.64 - 3.21: 8425 3.21 - 3.77: 13356 3.77 - 4.34: 18442 4.34 - 4.90: 29494 Nonbonded interactions: 69904 Sorted by model distance: nonbonded pdb=" O LYS A 83 " pdb=" NE2 GLN A 109 " model vdw 2.078 3.120 nonbonded pdb=" NE2 GLN A 470 " pdb=" OG1 THR A 472 " model vdw 2.109 3.120 nonbonded pdb=" OE1 GLU A 719 " pdb=" NH1 ARG A 739 " model vdw 2.133 3.120 nonbonded pdb=" OG1 THR A 780 " pdb=" OE2 GLU A 784 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR A 984 " pdb=" OE2 GLU A 988 " model vdw 2.151 3.040 ... (remaining 69899 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.004 0.048 9100 Z= 0.206 Angle : 0.971 8.822 12326 Z= 0.543 Chirality : 0.054 0.262 1424 Planarity : 0.006 0.063 1587 Dihedral : 12.793 86.940 3367 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.22), residues: 1131 helix: -2.15 (0.51), residues: 68 sheet: -1.34 (0.24), residues: 418 loop : -3.19 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.002 ARG A 739 TYR 0.022 0.002 TYR A 726 PHE 0.030 0.002 PHE A 67 TRP 0.015 0.002 TRP A 207 HIS 0.014 0.002 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9099) covalent geometry : angle 0.97125 (12324) SS BOND : bond 0.00101 ( 1) SS BOND : angle 1.56577 ( 2) hydrogen bonds : bond 0.27555 ( 228) hydrogen bonds : angle 10.15033 ( 636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 1081 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7486 (tmtm) outliers start: 0 outliers final: 1 residues processed: 129 average time/residue: 0.6071 time to fit residues: 82.9751 Evaluate side-chains 69 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 HIS A 677 ASN A 852 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.164249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.122262 restraints weight = 22861.196| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 5.40 r_work: 0.4003 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9100 Z= 0.155 Angle : 0.803 9.681 12326 Z= 0.408 Chirality : 0.052 0.319 1424 Planarity : 0.006 0.082 1587 Dihedral : 6.686 79.079 1222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.60 % Allowed : 9.59 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.22), residues: 1131 helix: -1.68 (0.57), residues: 80 sheet: -1.23 (0.24), residues: 438 loop : -3.03 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 739 TYR 0.017 0.002 TYR A 91 PHE 0.020 0.002 PHE A 965 TRP 0.011 0.002 TRP A 561 HIS 0.016 0.001 HIS A1070 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9099) covalent geometry : angle 0.80194 (12324) SS BOND : bond 0.00267 ( 1) SS BOND : angle 2.62076 ( 2) hydrogen bonds : bond 0.04651 ( 228) hydrogen bonds : angle 7.04180 ( 636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3567 (ptp) REVERT: A 691 LEU cc_start: 0.8385 (mm) cc_final: 0.8103 (pt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.4835 time to fit residues: 48.9905 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 ASN A1140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.114707 restraints weight = 22704.981| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 5.10 r_work: 0.3876 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9100 Z= 0.275 Angle : 0.852 9.398 12326 Z= 0.438 Chirality : 0.054 0.387 1424 Planarity : 0.006 0.078 1587 Dihedral : 6.894 77.925 1222 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.20 % Allowed : 12.99 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.22), residues: 1131 helix: -2.49 (0.49), residues: 78 sheet: -1.08 (0.24), residues: 425 loop : -3.14 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 739 TYR 0.024 0.002 TYR A 3 PHE 0.020 0.002 PHE A 382 TRP 0.015 0.002 TRP A 561 HIS 0.012 0.002 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 9099) covalent geometry : angle 0.85168 (12324) SS BOND : bond 0.00299 ( 1) SS BOND : angle 2.55712 ( 2) hydrogen bonds : bond 0.05315 ( 228) hydrogen bonds : angle 7.07205 ( 636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6596 (ptp) REVERT: A 218 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6890 (ttt) REVERT: A 338 VAL cc_start: 0.7547 (m) cc_final: 0.7232 (t) REVERT: A 534 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.3881 (ptp) REVERT: A 668 PHE cc_start: 0.8242 (m-10) cc_final: 0.7870 (t80) REVERT: A 929 SER cc_start: 0.8120 (m) cc_final: 0.7918 (m) outliers start: 32 outliers final: 12 residues processed: 95 average time/residue: 0.4450 time to fit residues: 45.8812 Evaluate side-chains 78 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.161389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.119404 restraints weight = 22881.769| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 5.10 r_work: 0.3956 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9100 Z= 0.131 Angle : 0.711 9.095 12326 Z= 0.362 Chirality : 0.050 0.337 1424 Planarity : 0.005 0.061 1587 Dihedral : 5.812 20.357 1220 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.20 % Allowed : 16.48 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.22), residues: 1131 helix: -1.97 (0.52), residues: 86 sheet: -0.93 (0.25), residues: 422 loop : -3.09 (0.20), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1080 TYR 0.020 0.001 TYR A 91 PHE 0.025 0.002 PHE A 140 TRP 0.011 0.001 TRP A 561 HIS 0.012 0.001 HIS A1070 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9099) covalent geometry : angle 0.71026 (12324) SS BOND : bond 0.00065 ( 1) SS BOND : angle 1.62475 ( 2) hydrogen bonds : bond 0.03694 ( 228) hydrogen bonds : angle 6.31713 ( 636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6136 (ptp) REVERT: A 333 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6761 (tp) REVERT: A 538 VAL cc_start: 0.4770 (OUTLIER) cc_final: 0.4146 (t) REVERT: A 668 PHE cc_start: 0.8207 (m-10) cc_final: 0.7841 (t80) REVERT: A 679 MET cc_start: 0.5557 (ptt) cc_final: 0.4998 (ptt) REVERT: A 691 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7940 (pp) REVERT: A 789 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.5488 (m-70) outliers start: 32 outliers final: 11 residues processed: 87 average time/residue: 0.4809 time to fit residues: 45.5612 Evaluate side-chains 72 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 789 HIS Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 55 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 overall best weight: 3.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.157092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.114407 restraints weight = 22715.135| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 5.07 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9100 Z= 0.248 Angle : 0.788 9.252 12326 Z= 0.406 Chirality : 0.052 0.333 1424 Planarity : 0.006 0.062 1587 Dihedral : 6.133 23.505 1220 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 3.80 % Allowed : 17.18 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.22), residues: 1131 helix: -2.26 (0.49), residues: 86 sheet: -1.00 (0.24), residues: 415 loop : -3.13 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 739 TYR 0.021 0.002 TYR A 3 PHE 0.015 0.002 PHE A 382 TRP 0.012 0.002 TRP A 561 HIS 0.028 0.002 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9099) covalent geometry : angle 0.78760 (12324) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.95038 ( 2) hydrogen bonds : bond 0.04619 ( 228) hydrogen bonds : angle 6.69515 ( 636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6322 (ptp) REVERT: A 351 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: A 538 VAL cc_start: 0.4724 (OUTLIER) cc_final: 0.4444 (t) REVERT: A 712 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 950 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7756 (p0) outliers start: 38 outliers final: 16 residues processed: 90 average time/residue: 0.5041 time to fit residues: 49.2164 Evaluate side-chains 77 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 44 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS A 950 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.158116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.115807 restraints weight = 22790.291| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 5.04 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9100 Z= 0.176 Angle : 0.728 8.905 12326 Z= 0.373 Chirality : 0.050 0.328 1424 Planarity : 0.005 0.052 1587 Dihedral : 5.920 25.181 1220 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.80 % Allowed : 18.58 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.22), residues: 1131 helix: -2.04 (0.51), residues: 86 sheet: -0.93 (0.25), residues: 411 loop : -3.08 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 147 TYR 0.019 0.001 TYR A 91 PHE 0.050 0.002 PHE A 668 TRP 0.013 0.002 TRP A 561 HIS 0.009 0.001 HIS A1070 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9099) covalent geometry : angle 0.72740 (12324) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.53522 ( 2) hydrogen bonds : bond 0.03927 ( 228) hydrogen bonds : angle 6.42337 ( 636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.369 Fit side-chains REVERT: A 130 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6224 (ptp) REVERT: A 351 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: A 538 VAL cc_start: 0.4695 (OUTLIER) cc_final: 0.4468 (t) REVERT: A 659 ILE cc_start: 0.8903 (mp) cc_final: 0.8561 (mm) REVERT: A 679 MET cc_start: 0.4980 (ptt) cc_final: 0.4328 (ptt) REVERT: A 691 LEU cc_start: 0.8389 (mm) cc_final: 0.7919 (pp) REVERT: A 712 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8971 (mp) outliers start: 38 outliers final: 19 residues processed: 90 average time/residue: 0.4273 time to fit residues: 42.2989 Evaluate side-chains 77 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS A 950 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.159465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.117678 restraints weight = 22762.873| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 5.04 r_work: 0.3929 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9100 Z= 0.139 Angle : 0.690 9.371 12326 Z= 0.353 Chirality : 0.049 0.315 1424 Planarity : 0.005 0.050 1587 Dihedral : 5.597 19.354 1220 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.80 % Allowed : 19.78 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.23), residues: 1131 helix: -1.75 (0.52), residues: 86 sheet: -0.83 (0.25), residues: 398 loop : -2.91 (0.20), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 147 TYR 0.018 0.001 TYR A 91 PHE 0.035 0.002 PHE A 668 TRP 0.012 0.001 TRP A 561 HIS 0.009 0.001 HIS A1070 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9099) covalent geometry : angle 0.68957 (12324) SS BOND : bond 0.00061 ( 1) SS BOND : angle 1.35617 ( 2) hydrogen bonds : bond 0.03489 ( 228) hydrogen bonds : angle 6.15010 ( 636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.297 Fit side-chains REVERT: A 130 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6162 (ptp) REVERT: A 351 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: A 534 MET cc_start: 0.3591 (ptp) cc_final: 0.0245 (ptt) REVERT: A 659 ILE cc_start: 0.8836 (mp) cc_final: 0.8509 (mm) REVERT: A 679 MET cc_start: 0.5353 (ptt) cc_final: 0.4943 (ptt) REVERT: A 691 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7909 (pp) REVERT: A 950 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7880 (p0) REVERT: A 1081 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7659 (tptt) REVERT: A 1105 MET cc_start: 0.7335 (ptt) cc_final: 0.6951 (ppp) outliers start: 38 outliers final: 15 residues processed: 87 average time/residue: 0.4783 time to fit residues: 45.3292 Evaluate side-chains 71 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 55 optimal weight: 50.0000 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.116765 restraints weight = 22763.201| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 5.04 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9100 Z= 0.163 Angle : 0.720 9.962 12326 Z= 0.367 Chirality : 0.049 0.303 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.652 20.362 1220 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.30 % Allowed : 20.88 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.23), residues: 1131 helix: -1.75 (0.53), residues: 86 sheet: -0.83 (0.25), residues: 398 loop : -2.91 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 147 TYR 0.019 0.001 TYR A 91 PHE 0.029 0.002 PHE A 668 TRP 0.012 0.002 TRP A 561 HIS 0.012 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9099) covalent geometry : angle 0.72014 (12324) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.35417 ( 2) hydrogen bonds : bond 0.03708 ( 228) hydrogen bonds : angle 6.16478 ( 636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.376 Fit side-chains REVERT: A 130 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6082 (ptp) REVERT: A 351 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: A 534 MET cc_start: 0.2420 (ptp) cc_final: -0.1276 (ptt) REVERT: A 659 ILE cc_start: 0.8835 (mp) cc_final: 0.8471 (mm) REVERT: A 679 MET cc_start: 0.4954 (ptt) cc_final: 0.4303 (ptt) REVERT: A 691 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7856 (pp) REVERT: A 950 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7731 (p0) REVERT: A 1081 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7413 (tptp) REVERT: A 1105 MET cc_start: 0.7010 (ptt) cc_final: 0.6751 (ppp) outliers start: 33 outliers final: 18 residues processed: 82 average time/residue: 0.4808 time to fit residues: 42.9845 Evaluate side-chains 74 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.158781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.117011 restraints weight = 22736.441| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 4.96 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9100 Z= 0.150 Angle : 0.718 10.716 12326 Z= 0.364 Chirality : 0.049 0.294 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.559 19.980 1220 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.00 % Allowed : 21.78 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.23), residues: 1131 helix: -1.69 (0.54), residues: 86 sheet: -0.77 (0.25), residues: 405 loop : -2.89 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 147 TYR 0.015 0.001 TYR A 91 PHE 0.025 0.002 PHE A 668 TRP 0.012 0.002 TRP A 561 HIS 0.011 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9099) covalent geometry : angle 0.71812 (12324) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.27227 ( 2) hydrogen bonds : bond 0.03566 ( 228) hydrogen bonds : angle 6.08800 ( 636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.376 Fit side-chains REVERT: A 130 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6055 (ptp) REVERT: A 351 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 534 MET cc_start: 0.1576 (ptp) cc_final: -0.2284 (ptt) REVERT: A 659 ILE cc_start: 0.8782 (mp) cc_final: 0.8430 (mm) REVERT: A 679 MET cc_start: 0.4934 (ptt) cc_final: 0.4627 (ptt) REVERT: A 1081 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7403 (tptp) REVERT: A 1105 MET cc_start: 0.6938 (ptt) cc_final: 0.6717 (ppp) outliers start: 30 outliers final: 21 residues processed: 82 average time/residue: 0.4898 time to fit residues: 43.7107 Evaluate side-chains 78 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 111 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.158597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.116951 restraints weight = 22795.311| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 4.95 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9100 Z= 0.148 Angle : 0.720 11.156 12326 Z= 0.363 Chirality : 0.049 0.303 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.522 19.039 1220 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.90 % Allowed : 22.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.23), residues: 1131 helix: -1.68 (0.54), residues: 86 sheet: -0.74 (0.25), residues: 411 loop : -2.90 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 147 TYR 0.020 0.001 TYR A 91 PHE 0.023 0.002 PHE A 668 TRP 0.011 0.001 TRP A 561 HIS 0.012 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9099) covalent geometry : angle 0.71967 (12324) SS BOND : bond 0.00142 ( 1) SS BOND : angle 1.28360 ( 2) hydrogen bonds : bond 0.03525 ( 228) hydrogen bonds : angle 6.06024 ( 636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.354 Fit side-chains REVERT: A 130 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6138 (ptp) REVERT: A 218 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.5069 (tmm) REVERT: A 534 MET cc_start: 0.1609 (ptp) cc_final: -0.2168 (ptt) REVERT: A 659 ILE cc_start: 0.8839 (mp) cc_final: 0.8483 (mm) REVERT: A 679 MET cc_start: 0.4851 (ptt) cc_final: 0.4528 (ptt) REVERT: A 950 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7664 (p0) outliers start: 29 outliers final: 22 residues processed: 78 average time/residue: 0.4915 time to fit residues: 41.7514 Evaluate side-chains 77 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.0000 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 65 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.1886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** 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 = 0.4728 r_free = 0.4728 target = 0.158614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4153 r_free = 0.4153 target = 0.117139 restraints weight = 22457.126| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 4.98 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 9100 Z= 0.214 Angle : 1.014 59.132 12326 Z= 0.565 Chirality : 0.057 1.139 1424 Planarity : 0.005 0.052 1587 Dihedral : 5.538 19.425 1220 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.60 % Allowed : 22.28 % Favored : 75.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.23), residues: 1131 helix: -1.68 (0.54), residues: 86 sheet: -0.74 (0.25), residues: 411 loop : -2.89 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1102 TYR 0.019 0.001 TYR A 91 PHE 0.022 0.002 PHE A 668 TRP 0.011 0.001 TRP A 561 HIS 0.011 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9099) covalent geometry : angle 1.01387 (12324) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.25519 ( 2) hydrogen bonds : bond 0.03518 ( 228) hydrogen bonds : angle 6.06503 ( 636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4337.82 seconds wall clock time: 74 minutes 35.52 seconds (4475.52 seconds total)