Starting phenix.real_space_refine on Sun Jul 27 03:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6k_61175/07_2025/9j6k_61175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6k_61175/07_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_61175/07_2025/9j6k_61175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6k_61175/07_2025/9j6k_61175.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6k_61175/07_2025/9j6k_61175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6k_61175/07_2025/9j6k_61175.cif" } resolution = 2.68 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.63 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: 2.03 Conformation dependent library (CDL) restraints added in 994.1 milliseconds 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: 1.29 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: 3.80 Time building geometry restraints manager: 2.45 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: 2.420 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- 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 : 23.12 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 (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: -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 TRP 0.015 0.002 TRP A 207 HIS 0.014 0.002 HIS A 789 PHE 0.030 0.002 PHE A 67 TYR 0.022 0.002 TYR A 726 ARG 0.044 0.002 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.27555 ( 228) hydrogen bonds : angle 10.15033 ( 636) SS BOND : bond 0.00101 ( 1) SS BOND : angle 1.56577 ( 2) covalent geometry : bond 0.00422 ( 9099) covalent geometry : angle 0.97125 (12324) *********************** 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 : 0.918 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: 1.3150 time to fit residues: 180.4362 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 : 0.923 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 overall best weight: 3.1484 ------------------------------------------------------------------------------- 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 470 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 HIS A 677 ASN A1034 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.159405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.116593 restraints weight = 22593.630| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 5.11 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9100 Z= 0.251 Angle : 0.879 10.518 12326 Z= 0.451 Chirality : 0.054 0.307 1424 Planarity : 0.007 0.075 1587 Dihedral : 7.126 81.987 1222 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.90 % Allowed : 10.99 % Favored : 87.11 % 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: -3.44 (0.22), residues: 1131 helix: -2.00 (0.55), residues: 72 sheet: -1.33 (0.24), residues: 434 loop : -3.15 (0.20), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.014 0.002 HIS A1070 PHE 0.022 0.003 PHE A 965 TYR 0.020 0.002 TYR A 5 ARG 0.012 0.001 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 228) hydrogen bonds : angle 7.32751 ( 636) SS BOND : bond 0.00356 ( 1) SS BOND : angle 3.15396 ( 2) covalent geometry : bond 0.00584 ( 9099) covalent geometry : angle 0.87822 (12324) *********************** 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 99 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 VAL cc_start: 0.7725 (m) cc_final: 0.7305 (m) REVERT: A 534 MET cc_start: 0.3690 (OUTLIER) cc_final: 0.3062 (ptp) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 1.1054 time to fit residues: 107.7791 Evaluate side-chains 79 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 302 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** 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** ** A1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.156160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.113319 restraints weight = 22789.760| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 5.13 r_work: 0.3848 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9100 Z= 0.300 Angle : 0.870 9.382 12326 Z= 0.449 Chirality : 0.054 0.279 1424 Planarity : 0.007 0.077 1587 Dihedral : 6.692 27.714 1220 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 3.80 % Allowed : 13.19 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.22), residues: 1131 helix: -2.67 (0.46), residues: 83 sheet: -1.21 (0.24), residues: 426 loop : -3.32 (0.20), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 207 HIS 0.012 0.002 HIS A1070 PHE 0.037 0.003 PHE A 668 TYR 0.027 0.003 TYR A 3 ARG 0.009 0.001 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 228) hydrogen bonds : angle 7.31352 ( 636) SS BOND : bond 0.00257 ( 1) SS BOND : angle 2.70542 ( 2) covalent geometry : bond 0.00690 ( 9099) covalent geometry : angle 0.86892 (12324) *********************** 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 112 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6662 (ptp) REVERT: A 218 MET cc_start: 0.7728 (tpp) cc_final: 0.7254 (ttt) REVERT: A 538 VAL cc_start: 0.5102 (OUTLIER) cc_final: 0.4375 (t) outliers start: 38 outliers final: 11 residues processed: 99 average time/residue: 1.2824 time to fit residues: 138.1648 Evaluate side-chains 74 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 102 THR 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 538 VAL Chi-restraints excluded: chain A residue 801 VAL 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 1136 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ** 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 = 0.4731 r_free = 0.4731 target = 0.159073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.116670 restraints weight = 22848.837| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 5.12 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9100 Z= 0.153 Angle : 0.735 9.436 12326 Z= 0.377 Chirality : 0.050 0.253 1424 Planarity : 0.006 0.070 1587 Dihedral : 6.052 20.909 1220 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.50 % Allowed : 17.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.34 (0.22), residues: 1131 helix: -2.19 (0.48), residues: 86 sheet: -1.16 (0.24), residues: 428 loop : -3.12 (0.20), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 207 HIS 0.012 0.001 HIS A1070 PHE 0.025 0.002 PHE A 140 TYR 0.020 0.001 TYR A 91 ARG 0.009 0.001 ARG A1080 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 228) hydrogen bonds : angle 6.63756 ( 636) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.87714 ( 2) covalent geometry : bond 0.00353 ( 9099) covalent geometry : angle 0.73436 (12324) *********************** 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 93 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6212 (ptp) REVERT: A 218 MET cc_start: 0.7550 (tpp) cc_final: 0.7248 (ttm) REVERT: A 351 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: A 534 MET cc_start: 0.3840 (ptp) cc_final: 0.3433 (ptp) REVERT: A 679 MET cc_start: 0.5134 (ptt) cc_final: 0.4577 (ptt) REVERT: A 691 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7852 (pp) outliers start: 25 outliers final: 16 residues processed: 84 average time/residue: 0.9480 time to fit residues: 87.1359 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU 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 333 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 691 LEU 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 923 VAL 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 1139 ILE Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.158990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.116586 restraints weight = 22610.530| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 5.10 r_work: 0.3909 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9100 Z= 0.152 Angle : 0.712 9.047 12326 Z= 0.364 Chirality : 0.049 0.230 1424 Planarity : 0.005 0.065 1587 Dihedral : 5.791 20.610 1220 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 3.30 % Allowed : 18.48 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.15 (0.22), residues: 1131 helix: -2.02 (0.50), residues: 86 sheet: -0.87 (0.25), residues: 404 loop : -3.07 (0.20), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.010 0.001 HIS A1070 PHE 0.027 0.002 PHE A 668 TYR 0.019 0.001 TYR A 91 ARG 0.015 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 228) hydrogen bonds : angle 6.39450 ( 636) SS BOND : bond 0.00152 ( 1) SS BOND : angle 1.66703 ( 2) covalent geometry : bond 0.00354 ( 9099) covalent geometry : angle 0.71223 (12324) *********************** 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 89 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6276 (ptp) REVERT: A 333 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6817 (tp) REVERT: A 351 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: A 538 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4352 (t) REVERT: A 659 ILE cc_start: 0.8854 (mp) cc_final: 0.8521 (mm) REVERT: A 679 MET cc_start: 0.5604 (ptt) cc_final: 0.4919 (ptt) REVERT: A 691 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7867 (pp) REVERT: B 88 ILE cc_start: 0.8912 (mp) cc_final: 0.8505 (tp) outliers start: 33 outliers final: 14 residues processed: 78 average time/residue: 1.0178 time to fit residues: 86.9488 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 304 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 691 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 962 ASP 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 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 41 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 664 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.157296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.114823 restraints weight = 22608.015| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 5.12 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9100 Z= 0.187 Angle : 0.724 10.226 12326 Z= 0.370 Chirality : 0.049 0.233 1424 Planarity : 0.005 0.055 1587 Dihedral : 5.843 20.946 1220 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.50 % Allowed : 18.88 % 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 (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: -3.14 (0.22), residues: 1131 helix: -1.94 (0.50), residues: 85 sheet: -0.97 (0.25), residues: 397 loop : -2.97 (0.20), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 561 HIS 0.009 0.001 HIS A1070 PHE 0.013 0.002 PHE A 382 TYR 0.020 0.002 TYR A 91 ARG 0.009 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 228) hydrogen bonds : angle 6.44007 ( 636) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.62128 ( 2) covalent geometry : bond 0.00435 ( 9099) covalent geometry : angle 0.72400 (12324) *********************** 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 96 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6227 (ptp) REVERT: A 351 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: A 538 VAL cc_start: 0.4675 (OUTLIER) cc_final: 0.4406 (t) REVERT: A 691 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 103 MET cc_start: 0.7009 (ptt) cc_final: 0.6799 (ptt) outliers start: 35 outliers final: 19 residues processed: 87 average time/residue: 0.8824 time to fit residues: 84.6195 Evaluate side-chains 76 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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 691 LEU 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 962 ASP 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 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 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.159236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.117423 restraints weight = 22638.222| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 5.06 r_work: 0.3925 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9100 Z= 0.132 Angle : 0.690 9.442 12326 Z= 0.351 Chirality : 0.048 0.225 1424 Planarity : 0.005 0.052 1587 Dihedral : 5.531 19.587 1220 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.40 % Allowed : 19.98 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.95 (0.22), residues: 1131 helix: -1.71 (0.52), residues: 86 sheet: -0.88 (0.25), residues: 391 loop : -2.81 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 411 HIS 0.009 0.001 HIS A1070 PHE 0.023 0.002 PHE A 668 TYR 0.019 0.001 TYR A 91 ARG 0.006 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 228) hydrogen bonds : angle 6.10649 ( 636) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.32530 ( 2) covalent geometry : bond 0.00306 ( 9099) covalent geometry : angle 0.68998 (12324) *********************** 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 96 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6167 (ptp) REVERT: A 351 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: A 437 MET cc_start: -0.1583 (tpt) cc_final: -0.1856 (tmt) REVERT: A 534 MET cc_start: 0.4014 (ptp) cc_final: 0.0907 (ptt) REVERT: A 679 MET cc_start: 0.5372 (ptt) cc_final: 0.4581 (ptt) REVERT: A 691 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7822 (pp) REVERT: A 864 LYS cc_start: 0.7754 (tppt) cc_final: 0.7459 (tppt) REVERT: A 925 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5536 (t70) outliers start: 34 outliers final: 16 residues processed: 89 average time/residue: 0.9673 time to fit residues: 94.5259 Evaluate side-chains 76 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 304 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 691 LEU 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 925 ASP 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 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** 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 = 0.4740 r_free = 0.4740 target = 0.159525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.117946 restraints weight = 22838.112| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 5.03 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9100 Z= 0.126 Angle : 0.682 10.112 12326 Z= 0.346 Chirality : 0.048 0.221 1424 Planarity : 0.005 0.054 1587 Dihedral : 5.372 18.774 1220 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.80 % Allowed : 20.88 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.80 (0.23), residues: 1131 helix: -1.47 (0.54), residues: 86 sheet: -0.84 (0.25), residues: 398 loop : -2.71 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.009 0.001 HIS A1070 PHE 0.016 0.001 PHE A 614 TYR 0.014 0.001 TYR A 91 ARG 0.005 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 228) hydrogen bonds : angle 5.89259 ( 636) SS BOND : bond 0.00065 ( 1) SS BOND : angle 1.27916 ( 2) covalent geometry : bond 0.00293 ( 9099) covalent geometry : angle 0.68171 (12324) *********************** 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: 28 poor density : 60 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6045 (ptp) REVERT: A 534 MET cc_start: 0.1166 (ptp) cc_final: -0.2567 (ptt) REVERT: A 659 ILE cc_start: 0.8784 (mp) cc_final: 0.8398 (mm) REVERT: A 679 MET cc_start: 0.4760 (ptt) cc_final: 0.4071 (ptt) REVERT: A 691 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7615 (pp) REVERT: A 864 LYS cc_start: 0.7604 (tppt) cc_final: 0.7376 (tppt) REVERT: A 925 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5293 (t70) outliers start: 28 outliers final: 16 residues processed: 82 average time/residue: 1.3414 time to fit residues: 120.3623 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 569 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 905 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 = 0.4725 r_free = 0.4725 target = 0.158413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.116053 restraints weight = 22997.221| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 5.16 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9100 Z= 0.154 Angle : 0.712 10.620 12326 Z= 0.359 Chirality : 0.048 0.221 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.467 19.275 1220 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.30 % Allowed : 21.98 % Favored : 75.72 % 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: -2.88 (0.23), residues: 1131 helix: -1.72 (0.51), residues: 86 sheet: -0.92 (0.25), residues: 393 loop : -2.70 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.008 0.001 HIS A1070 PHE 0.018 0.002 PHE A 668 TYR 0.020 0.001 TYR A 91 ARG 0.006 0.001 ARG A1102 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 228) hydrogen bonds : angle 6.03415 ( 636) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.32297 ( 2) covalent geometry : bond 0.00361 ( 9099) covalent geometry : angle 0.71189 (12324) *********************** 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 80 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6080 (ptp) REVERT: A 534 MET cc_start: 0.2543 (ptp) cc_final: -0.1073 (ptt) REVERT: A 659 ILE cc_start: 0.8809 (mp) cc_final: 0.8424 (mm) REVERT: A 679 MET cc_start: 0.4916 (ptt) cc_final: 0.4586 (ptt) REVERT: A 691 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 864 LYS cc_start: 0.7651 (tppt) cc_final: 0.7434 (tppt) REVERT: A 925 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5385 (t70) outliers start: 23 outliers final: 16 residues processed: 75 average time/residue: 1.0404 time to fit residues: 85.3652 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 569 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 905 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 = 0.4736 r_free = 0.4736 target = 0.158945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.117425 restraints weight = 22724.187| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 5.10 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9100 Z= 0.133 Angle : 0.706 11.074 12326 Z= 0.354 Chirality : 0.048 0.221 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.375 19.130 1220 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.20 % Allowed : 22.08 % Favored : 75.72 % 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: -2.90 (0.23), residues: 1131 helix: -1.71 (0.52), residues: 87 sheet: -0.90 (0.25), residues: 405 loop : -2.76 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.009 0.001 HIS A1070 PHE 0.014 0.001 PHE A 614 TYR 0.020 0.001 TYR A 91 ARG 0.005 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 228) hydrogen bonds : angle 5.91289 ( 636) SS BOND : bond 0.00091 ( 1) SS BOND : angle 1.23320 ( 2) covalent geometry : bond 0.00312 ( 9099) covalent geometry : angle 0.70607 (12324) ********************** 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 82 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6062 (ptp) REVERT: A 534 MET cc_start: 0.1845 (ptp) cc_final: -0.1861 (ptt) REVERT: A 659 ILE cc_start: 0.8808 (mp) cc_final: 0.8428 (mm) REVERT: A 679 MET cc_start: 0.4804 (ptt) cc_final: 0.4486 (ptt) REVERT: A 691 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 864 LYS cc_start: 0.7630 (tppt) cc_final: 0.7423 (tppt) REVERT: A 875 GLU cc_start: 0.8097 (pp20) cc_final: 0.7493 (tm-30) REVERT: A 925 ASP cc_start: 0.5637 (OUTLIER) cc_final: 0.5359 (t70) REVERT: B 103 MET cc_start: 0.6683 (ptt) cc_final: 0.6406 (ptt) outliers start: 22 outliers final: 16 residues processed: 76 average time/residue: 1.3814 time to fit residues: 114.1296 Evaluate side-chains 75 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 569 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 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 = 0.4728 r_free = 0.4728 target = 0.158494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.116297 restraints weight = 23046.313| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 5.11 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9100 Z= 0.149 Angle : 0.722 11.186 12326 Z= 0.361 Chirality : 0.048 0.224 1424 Planarity : 0.005 0.053 1587 Dihedral : 5.401 19.170 1220 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.30 % Allowed : 22.68 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.92 (0.23), residues: 1131 helix: -1.76 (0.50), residues: 86 sheet: -0.89 (0.25), residues: 401 loop : -2.78 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.008 0.001 HIS A1070 PHE 0.022 0.002 PHE A 668 TYR 0.014 0.001 TYR A 91 ARG 0.005 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 228) hydrogen bonds : angle 6.01129 ( 636) SS BOND : bond 0.00151 ( 1) SS BOND : angle 1.30066 ( 2) covalent geometry : bond 0.00350 ( 9099) covalent geometry : angle 0.72193 (12324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8927.99 seconds wall clock time: 155 minutes 38.60 seconds (9338.60 seconds total)