Starting phenix.real_space_refine on Thu May 15 08:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.map" model { file = "/net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isi_35691/05_2025/8isi_35691.cif" } resolution = 3.77 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= 0.001 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 102 5.16 5 C 8319 2.51 5 N 2236 2.21 5 O 2438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13095 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6581 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 32, 'TRANS': 809} Chain breaks: 5 Chain: "B" Number of atoms: 6514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6514 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 32, 'TRANS': 800} Chain breaks: 5 Time building chain proxies: 6.94, per 1000 atoms: 0.53 Number of scatterers: 13095 At special positions: 0 Unit cell: (123.25, 129.2, 132.6, 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 102 16.00 O 2438 8.00 N 2236 7.00 C 8319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 16 sheets defined 42.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.579A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 154 removed outlier: 4.016A pdb=" N ASN A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.509A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 removed outlier: 3.701A pdb=" N LYS A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.628A pdb=" N TYR A 327 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 424 removed outlier: 3.530A pdb=" N ARG A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.557A pdb=" N LEU A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 569 through 590 removed outlier: 3.599A pdb=" N MET A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.727A pdb=" N PHE A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 924 Proline residue: A 910 - end of helix removed outlier: 3.595A pdb=" N THR A 924 " --> pdb=" O MET A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 Processing helix chain 'A' and resid 952 through 959 removed outlier: 4.294A pdb=" N ILE A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 988 removed outlier: 3.875A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N MET A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.674A pdb=" N LEU A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1073 removed outlier: 3.748A pdb=" N PHE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1096 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 134 through 147 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.510A pdb=" N SER B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 322 through 332 removed outlier: 3.518A pdb=" N GLN B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 327 " --> pdb=" O CYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 421 removed outlier: 3.547A pdb=" N ALA B 391 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 435 removed outlier: 4.330A pdb=" N ILE B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'B' and resid 569 through 590 removed outlier: 3.904A pdb=" N MET B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.565A pdb=" N VAL B 793 " --> pdb=" O LYS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.607A pdb=" N PHE B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 893 removed outlier: 3.926A pdb=" N VAL B 885 " --> pdb=" O GLN B 881 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 886 " --> pdb=" O ALA B 882 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 893 " --> pdb=" O ALA B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 removed outlier: 3.585A pdb=" N LYS B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 900 " --> pdb=" O ARG B 896 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 901 " --> pdb=" O LEU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 923 removed outlier: 3.630A pdb=" N LEU B 911 " --> pdb=" O ILE B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 3.990A pdb=" N ASP B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.611A pdb=" N GLN B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1009 through 1025 Processing helix chain 'B' and resid 1065 through 1073 Processing helix chain 'B' and resid 1080 through 1096 removed outlier: 3.553A pdb=" N SER B1085 " --> pdb=" O GLU B1081 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 240 removed outlier: 7.020A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 458 removed outlier: 3.664A pdb=" N TRP A 457 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 450 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 447 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY A 484 " --> pdb=" O THR A 746 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.238A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 858 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AA7, first strand: chain 'A' and resid 966 through 968 Processing sheet with id=AA8, first strand: chain 'A' and resid 991 through 994 removed outlier: 6.342A pdb=" N ARG A 991 " --> pdb=" O LEU A1033 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A1035 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 993 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ALA A1037 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN A1032 " --> pdb=" O THR A1060 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.828A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR B 99 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 86 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 183 " --> pdb=" O TYR B 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 250 through 257 removed outlier: 7.079A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 250 through 257 removed outlier: 7.079A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.442A pdb=" N GLY B 484 " --> pdb=" O PHE B 745 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.513A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 852 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 855 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 835 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'B' and resid 966 through 969 removed outlier: 3.768A pdb=" N LYS B 966 " --> pdb=" O GLY B1007 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B1007 " --> pdb=" O LYS B 966 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 968 " --> pdb=" O LEU B1005 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B1005 " --> pdb=" O PHE B 968 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 994 removed outlier: 4.625A pdb=" N GLN B1032 " --> pdb=" O THR B1060 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 3.50 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: 4082 1.34 - 1.46: 1893 1.46 - 1.58: 7189 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 13328 Sorted by residual: bond pdb=" N VAL B 793 " pdb=" CA VAL B 793 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.38e+00 bond pdb=" C ASN B 758 " pdb=" N PRO B 759 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.30e-02 5.92e+03 7.20e+00 bond pdb=" N GLU B 105 " pdb=" CA GLU B 105 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.84e+00 bond pdb=" N GLY A 533 " pdb=" CA GLY A 533 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.23e-02 6.61e+03 6.47e+00 bond pdb=" N HIS B 172 " pdb=" CA HIS B 172 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.06e+00 ... (remaining 13323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 17831 2.66 - 5.31: 141 5.31 - 7.96: 17 7.96 - 10.62: 3 10.62 - 13.27: 1 Bond angle restraints: 17993 Sorted by residual: angle pdb=" CA LEU A 430 " pdb=" CB LEU A 430 " pdb=" CG LEU A 430 " ideal model delta sigma weight residual 116.30 129.57 -13.27 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA LYS B 807 " pdb=" CB LYS B 807 " pdb=" CG LYS B 807 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CA GLY A 533 " pdb=" C GLY A 533 " pdb=" O GLY A 533 " ideal model delta sigma weight residual 122.47 118.61 3.86 1.08e+00 8.57e-01 1.28e+01 angle pdb=" CA MET B1096 " pdb=" CB MET B1096 " pdb=" CG MET B1096 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" C PRO B 759 " pdb=" CA PRO B 759 " pdb=" CB PRO B 759 " ideal model delta sigma weight residual 111.46 107.26 4.20 1.29e+00 6.01e-01 1.06e+01 ... (remaining 17988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7217 17.57 - 35.13: 718 35.13 - 52.70: 154 52.70 - 70.27: 25 70.27 - 87.83: 10 Dihedral angle restraints: 8124 sinusoidal: 3281 harmonic: 4843 Sorted by residual: dihedral pdb=" CA MET B 518 " pdb=" C MET B 518 " pdb=" N ILE B 519 " pdb=" CA ILE B 519 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP B 90 " pdb=" CB ASP B 90 " pdb=" CG ASP B 90 " pdb=" OD1 ASP B 90 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA VAL A 981 " pdb=" C VAL A 981 " pdb=" N MET A 982 " pdb=" CA MET A 982 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1581 0.040 - 0.080: 346 0.080 - 0.120: 123 0.120 - 0.161: 19 0.161 - 0.201: 2 Chirality restraints: 2071 Sorted by residual: chirality pdb=" CA VAL B 793 " pdb=" N VAL B 793 " pdb=" C VAL B 793 " pdb=" CB VAL B 793 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA HIS B 172 " pdb=" N HIS B 172 " pdb=" C HIS B 172 " pdb=" CB HIS B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA TYR A 385 " pdb=" N TYR A 385 " pdb=" C TYR A 385 " pdb=" CB TYR A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2068 not shown) Planarity restraints: 2293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 758 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ASN B 758 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 758 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 759 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 462 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO A 463 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 481 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C ASP A 481 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP A 481 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 482 " 0.011 2.00e-02 2.50e+03 ... (remaining 2290 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 203 2.68 - 3.24: 12133 3.24 - 3.79: 19114 3.79 - 4.35: 24006 4.35 - 4.90: 40983 Nonbonded interactions: 96439 Sorted by model distance: nonbonded pdb=" OE1 GLN A 930 " pdb=" OG1 THR B 924 " model vdw 2.128 3.040 nonbonded pdb=" OG SER B 213 " pdb=" OE1 GLU B1077 " model vdw 2.171 3.040 nonbonded pdb=" O SER A 104 " pdb=" OG1 THR A 108 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 100 " pdb=" OD1 ASN A 102 " model vdw 2.217 3.040 nonbonded pdb=" N GLU A 835 " pdb=" OE1 GLU A 835 " model vdw 2.232 3.120 ... (remaining 96434 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 347 or resid 361 through 534 or resid 562 throu \ gh 1039 or resid 1052 through 1119)) selection = (chain 'B' and (resid 75 through 109 or resid 120 through 347 or resid 361 throu \ gh 1119)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.410 Find NCS groups from input model: 0.530 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.003 0.071 13328 Z= 0.149 Angle : 0.605 13.275 17993 Z= 0.323 Chirality : 0.040 0.201 2071 Planarity : 0.004 0.050 2293 Dihedral : 14.570 87.835 4980 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.07 % Allowed : 14.64 % Favored : 85.29 % 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: 1.00 (0.22), residues: 1651 helix: 2.29 (0.20), residues: 667 sheet: 0.43 (0.28), residues: 362 loop : -1.04 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.011 0.001 HIS A 172 PHE 0.015 0.001 PHE A 869 TYR 0.022 0.001 TYR A 99 ARG 0.004 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.12888 ( 671) hydrogen bonds : angle 5.33600 ( 1938) covalent geometry : bond 0.00289 (13328) covalent geometry : angle 0.60539 (17993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 MET cc_start: 0.7553 (mmt) cc_final: 0.7303 (mmt) REVERT: A 920 MET cc_start: 0.7535 (tpt) cc_final: 0.6971 (tpp) REVERT: B 455 LYS cc_start: 0.7618 (tttp) cc_final: 0.7347 (ttmm) REVERT: B 1001 MET cc_start: 0.3273 (mmm) cc_final: 0.2241 (tpp) outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.2414 time to fit residues: 50.7864 Evaluate side-chains 137 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 172 HIS A 757 GLN A 873 GLN A 884 HIS A 941 GLN A1013 GLN A1059 HIS B 75 GLN B 826 ASN B 873 GLN B 880 GLN B 884 HIS B 980 GLN B1013 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.199072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175326 restraints weight = 16853.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171098 restraints weight = 26877.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169475 restraints weight = 31854.892| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13328 Z= 0.194 Angle : 0.590 6.923 17993 Z= 0.306 Chirality : 0.041 0.158 2071 Planarity : 0.004 0.049 2293 Dihedral : 4.373 55.506 1782 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.83 % Allowed : 14.85 % Favored : 82.32 % 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: 0.63 (0.21), residues: 1651 helix: 1.89 (0.20), residues: 685 sheet: 0.25 (0.28), residues: 370 loop : -1.24 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 778 HIS 0.008 0.001 HIS A 172 PHE 0.022 0.002 PHE A 869 TYR 0.030 0.002 TYR B 242 ARG 0.005 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 671) hydrogen bonds : angle 4.69928 ( 1938) covalent geometry : bond 0.00463 (13328) covalent geometry : angle 0.58958 (17993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.7520 (p) cc_final: 0.7286 (m) REVERT: A 157 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 518 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6682 (ptt) REVERT: B 983 MET cc_start: 0.5521 (tpp) cc_final: 0.5095 (tmm) REVERT: B 1001 MET cc_start: 0.2642 (mmm) cc_final: 0.1863 (tpp) outliers start: 41 outliers final: 24 residues processed: 174 average time/residue: 0.2217 time to fit residues: 57.8312 Evaluate side-chains 166 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 870 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1059 HIS B 142 GLN B 412 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.187715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151634 restraints weight = 17328.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150321 restraints weight = 27590.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149944 restraints weight = 25034.631| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 13328 Z= 0.359 Angle : 0.783 9.927 17993 Z= 0.411 Chirality : 0.048 0.250 2071 Planarity : 0.006 0.052 2293 Dihedral : 5.428 51.068 1782 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.46 % Allowed : 15.75 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1651 helix: 1.08 (0.19), residues: 677 sheet: -0.15 (0.28), residues: 370 loop : -1.72 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 778 HIS 0.012 0.002 HIS A 397 PHE 0.029 0.003 PHE A 869 TYR 0.045 0.003 TYR B 242 ARG 0.004 0.001 ARG B 523 Details of bonding type rmsd hydrogen bonds : bond 0.06986 ( 671) hydrogen bonds : angle 5.34814 ( 1938) covalent geometry : bond 0.00872 (13328) covalent geometry : angle 0.78264 (17993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 152 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7624 (tmm) cc_final: 0.7184 (tmm) REVERT: A 157 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 385 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 915 MET cc_start: 0.6799 (mmt) cc_final: 0.6524 (mmt) REVERT: B 416 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8250 (m) REVERT: B 432 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6196 (pt) REVERT: B 438 ASN cc_start: 0.7554 (t0) cc_final: 0.7330 (t0) REVERT: B 455 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7166 (tptp) REVERT: B 518 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7299 (ptt) REVERT: B 572 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: B 807 LYS cc_start: 0.8388 (tmtt) cc_final: 0.8135 (tmtt) outliers start: 79 outliers final: 49 residues processed: 217 average time/residue: 0.2377 time to fit residues: 77.8797 Evaluate side-chains 190 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1059 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 123 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 156 optimal weight: 30.0000 chunk 135 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 GLN A1059 HIS B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.197318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.173366 restraints weight = 16865.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168147 restraints weight = 29669.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167003 restraints weight = 41140.443| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13328 Z= 0.150 Angle : 0.581 7.974 17993 Z= 0.299 Chirality : 0.041 0.165 2071 Planarity : 0.004 0.055 2293 Dihedral : 4.723 51.520 1782 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.94 % Allowed : 19.13 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1651 helix: 1.64 (0.20), residues: 681 sheet: -0.18 (0.28), residues: 379 loop : -1.65 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 366 HIS 0.005 0.001 HIS A1059 PHE 0.020 0.002 PHE A 869 TYR 0.023 0.002 TYR B 242 ARG 0.003 0.000 ARG A 932 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 671) hydrogen bonds : angle 4.71103 ( 1938) covalent geometry : bond 0.00352 (13328) covalent geometry : angle 0.58130 (17993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7051 (tmm) cc_final: 0.6695 (tmm) REVERT: A 157 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 749 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: B 438 ASN cc_start: 0.7336 (t0) cc_final: 0.7063 (t0) REVERT: B 518 MET cc_start: 0.7275 (ppp) cc_final: 0.6895 (ptt) REVERT: B 1001 MET cc_start: 0.2389 (mmm) cc_final: 0.1757 (mtp) outliers start: 57 outliers final: 38 residues processed: 200 average time/residue: 0.2226 time to fit residues: 67.3489 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 166 optimal weight: 40.0000 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 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 779 ASN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.200127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177112 restraints weight = 16868.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173226 restraints weight = 28330.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172268 restraints weight = 36068.017| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13328 Z= 0.121 Angle : 0.551 7.932 17993 Z= 0.278 Chirality : 0.039 0.140 2071 Planarity : 0.004 0.051 2293 Dihedral : 4.352 52.654 1782 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.87 % Allowed : 19.68 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1651 helix: 1.90 (0.20), residues: 685 sheet: -0.02 (0.29), residues: 358 loop : -1.51 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 366 HIS 0.004 0.001 HIS B 249 PHE 0.016 0.001 PHE A 869 TYR 0.019 0.001 TYR B 242 ARG 0.003 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 671) hydrogen bonds : angle 4.44924 ( 1938) covalent geometry : bond 0.00277 (13328) covalent geometry : angle 0.55129 (17993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8565 (tt) REVERT: A 749 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: A 1001 MET cc_start: 0.3317 (tpt) cc_final: 0.2983 (tpt) REVERT: B 438 ASN cc_start: 0.7317 (t0) cc_final: 0.7025 (t0) REVERT: B 1001 MET cc_start: 0.2380 (mmm) cc_final: 0.1635 (mtp) outliers start: 56 outliers final: 33 residues processed: 190 average time/residue: 0.2266 time to fit residues: 63.8358 Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 160 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS B 467 HIS B1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.170672 restraints weight = 17317.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168437 restraints weight = 30442.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167512 restraints weight = 33461.205| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13328 Z= 0.267 Angle : 0.707 8.840 17993 Z= 0.359 Chirality : 0.044 0.196 2071 Planarity : 0.005 0.054 2293 Dihedral : 4.882 52.945 1782 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.70 % Allowed : 19.27 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1651 helix: 1.53 (0.19), residues: 683 sheet: -0.22 (0.28), residues: 377 loop : -1.75 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 778 HIS 0.008 0.001 HIS A 397 PHE 0.025 0.002 PHE A 869 TYR 0.034 0.002 TYR B 242 ARG 0.004 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.05822 ( 671) hydrogen bonds : angle 4.89577 ( 1938) covalent geometry : bond 0.00649 (13328) covalent geometry : angle 0.70720 (17993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 283 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7681 (ttt) REVERT: A 749 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: B 257 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6259 (p) REVERT: B 438 ASN cc_start: 0.7526 (t0) cc_final: 0.7254 (t0) REVERT: B 907 ILE cc_start: 0.5133 (OUTLIER) cc_final: 0.4748 (tp) REVERT: B 1001 MET cc_start: 0.2394 (mmm) cc_final: 0.1685 (mtp) outliers start: 68 outliers final: 55 residues processed: 193 average time/residue: 0.2275 time to fit residues: 66.4939 Evaluate side-chains 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1059 HIS Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 132 optimal weight: 3.9990 chunk 87 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.0010 chunk 145 optimal weight: 2.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.202043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178035 restraints weight = 16973.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175296 restraints weight = 27845.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.174008 restraints weight = 34071.072| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13328 Z= 0.106 Angle : 0.590 13.447 17993 Z= 0.289 Chirality : 0.039 0.136 2071 Planarity : 0.004 0.055 2293 Dihedral : 4.259 52.761 1782 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 21.82 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1651 helix: 1.97 (0.20), residues: 687 sheet: 0.07 (0.29), residues: 355 loop : -1.47 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.003 0.001 HIS B 249 PHE 0.014 0.001 PHE B 869 TYR 0.022 0.001 TYR A 902 ARG 0.005 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 671) hydrogen bonds : angle 4.34728 ( 1938) covalent geometry : bond 0.00226 (13328) covalent geometry : angle 0.59011 (17993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 438 ASN cc_start: 0.7412 (t0) cc_final: 0.7080 (t0) REVERT: B 485 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7681 (mm) REVERT: B 525 HIS cc_start: 0.5872 (t-90) cc_final: 0.5548 (t70) REVERT: B 982 MET cc_start: 0.7001 (tmm) cc_final: 0.6648 (mtt) REVERT: B 1001 MET cc_start: 0.2202 (mmm) cc_final: 0.1407 (mtp) outliers start: 39 outliers final: 26 residues processed: 172 average time/residue: 0.2368 time to fit residues: 60.9361 Evaluate side-chains 158 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 138 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.199897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176164 restraints weight = 17104.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.174650 restraints weight = 28968.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173930 restraints weight = 28754.527| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13328 Z= 0.129 Angle : 0.617 11.206 17993 Z= 0.303 Chirality : 0.039 0.146 2071 Planarity : 0.004 0.052 2293 Dihedral : 4.280 53.745 1782 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.90 % Allowed : 21.82 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1651 helix: 2.01 (0.20), residues: 687 sheet: 0.16 (0.29), residues: 354 loop : -1.53 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 366 HIS 0.003 0.001 HIS A 397 PHE 0.022 0.002 PHE A 280 TYR 0.019 0.001 TYR B 242 ARG 0.004 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 671) hydrogen bonds : angle 4.34839 ( 1938) covalent geometry : bond 0.00299 (13328) covalent geometry : angle 0.61660 (17993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: A 1087 MET cc_start: 0.5938 (tmm) cc_final: 0.5709 (tmm) REVERT: A 1096 MET cc_start: 0.3121 (OUTLIER) cc_final: 0.2645 (mmt) REVERT: B 438 ASN cc_start: 0.7450 (t0) cc_final: 0.7111 (t0) REVERT: B 518 MET cc_start: 0.7109 (ppp) cc_final: 0.6592 (ptm) REVERT: B 525 HIS cc_start: 0.5929 (t-90) cc_final: 0.5570 (t70) REVERT: B 982 MET cc_start: 0.6965 (tmm) cc_final: 0.6583 (mtt) REVERT: B 1001 MET cc_start: 0.2197 (mmm) cc_final: 0.1406 (mtp) outliers start: 42 outliers final: 36 residues processed: 170 average time/residue: 0.2343 time to fit residues: 60.0127 Evaluate side-chains 177 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 397 HIS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.195178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172215 restraints weight = 16993.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171035 restraints weight = 28161.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.170146 restraints weight = 31015.187| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13328 Z= 0.222 Angle : 0.703 10.697 17993 Z= 0.350 Chirality : 0.043 0.176 2071 Planarity : 0.004 0.054 2293 Dihedral : 4.693 53.204 1782 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.66 % Allowed : 21.34 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1651 helix: 1.72 (0.20), residues: 684 sheet: -0.00 (0.28), residues: 371 loop : -1.75 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 366 HIS 0.006 0.001 HIS A 397 PHE 0.022 0.002 PHE A 869 TYR 0.029 0.002 TYR B 242 ARG 0.005 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 671) hydrogen bonds : angle 4.72479 ( 1938) covalent geometry : bond 0.00540 (13328) covalent geometry : angle 0.70262 (17993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 TYR cc_start: 0.6671 (m-10) cc_final: 0.6460 (m-10) REVERT: A 283 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7661 (ttt) REVERT: A 749 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6551 (tt0) REVERT: A 1096 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.2797 (mmt) REVERT: B 438 ASN cc_start: 0.7537 (t0) cc_final: 0.7243 (t0) REVERT: B 907 ILE cc_start: 0.5130 (OUTLIER) cc_final: 0.4404 (mt) REVERT: B 982 MET cc_start: 0.7009 (tmm) cc_final: 0.6570 (mtt) REVERT: B 1001 MET cc_start: 0.2380 (mmm) cc_final: 0.1636 (mtp) outliers start: 53 outliers final: 41 residues processed: 175 average time/residue: 0.2281 time to fit residues: 60.5371 Evaluate side-chains 176 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 33 optimal weight: 0.0010 chunk 69 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177043 restraints weight = 16976.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176966 restraints weight = 28323.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176473 restraints weight = 26180.389| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13328 Z= 0.115 Angle : 0.626 11.608 17993 Z= 0.306 Chirality : 0.040 0.154 2071 Planarity : 0.004 0.055 2293 Dihedral : 4.260 52.972 1782 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.62 % Allowed : 22.17 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1651 helix: 1.95 (0.20), residues: 694 sheet: 0.16 (0.29), residues: 352 loop : -1.51 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.003 0.001 HIS B 577 PHE 0.029 0.001 PHE A 280 TYR 0.017 0.001 TYR B 242 ARG 0.005 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 671) hydrogen bonds : angle 4.33497 ( 1938) covalent geometry : bond 0.00254 (13328) covalent geometry : angle 0.62550 (17993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 MET cc_start: 0.8186 (tpt) cc_final: 0.7925 (tpt) REVERT: A 425 MET cc_start: 0.7983 (mmt) cc_final: 0.7645 (mmm) REVERT: A 1096 MET cc_start: 0.3012 (OUTLIER) cc_final: 0.2599 (mmt) REVERT: B 283 MET cc_start: 0.7351 (ttm) cc_final: 0.7047 (mtt) REVERT: B 438 ASN cc_start: 0.7472 (t0) cc_final: 0.7127 (t0) REVERT: B 518 MET cc_start: 0.7139 (ppp) cc_final: 0.6611 (ptt) REVERT: B 525 HIS cc_start: 0.5907 (t-90) cc_final: 0.5500 (t70) REVERT: B 982 MET cc_start: 0.6922 (tmm) cc_final: 0.6483 (mtt) REVERT: B 1001 MET cc_start: 0.2104 (mmm) cc_final: 0.1364 (mtp) outliers start: 38 outliers final: 34 residues processed: 164 average time/residue: 0.2225 time to fit residues: 55.3801 Evaluate side-chains 170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 745 PHE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 145 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.198867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175804 restraints weight = 16988.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172888 restraints weight = 28478.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172051 restraints weight = 30284.970| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13328 Z= 0.141 Angle : 0.637 11.392 17993 Z= 0.314 Chirality : 0.040 0.182 2071 Planarity : 0.004 0.053 2293 Dihedral : 4.311 54.126 1782 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 22.24 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1651 helix: 1.98 (0.20), residues: 688 sheet: 0.13 (0.29), residues: 360 loop : -1.56 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 366 HIS 0.004 0.001 HIS A 397 PHE 0.018 0.002 PHE A 869 TYR 0.021 0.002 TYR B 242 ARG 0.004 0.000 ARG A1011 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 671) hydrogen bonds : angle 4.39983 ( 1938) covalent geometry : bond 0.00333 (13328) covalent geometry : angle 0.63679 (17993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.05 seconds wall clock time: 60 minutes 52.26 seconds (3652.26 seconds total)