Starting phenix.real_space_refine on Sun Nov 17 05:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_35691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_35691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_35691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_35691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8isi_35691/11_2024/8isi_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-5513/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: 7.75, per 1000 atoms: 0.59 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: 3.34 Conformation dependent library (CDL) restraints added in 1.9 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: 1.51 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: 5.28 Time building geometry restraints manager: 3.79 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: 0.660 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.260 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- 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= 0.179 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 *********************** 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 : 1.559 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: 0.2835 time to fit residues: 60.2391 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 : 1.560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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= 0.298 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 *********************** 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 : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 915 MET cc_start: 0.7592 (mmt) cc_final: 0.7291 (mmt) REVERT: B 518 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7315 (ptt) REVERT: B 942 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7935 (mmtm) REVERT: B 983 MET cc_start: 0.5505 (tpp) cc_final: 0.5001 (tmm) REVERT: B 1001 MET cc_start: 0.3404 (mmm) cc_final: 0.2365 (tpp) outliers start: 41 outliers final: 24 residues processed: 174 average time/residue: 0.2336 time to fit residues: 60.9466 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 : 1.622 ------------------------------------------------------------------------------- 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 84 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.0670 chunk 164 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A1059 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13328 Z= 0.206 Angle : 0.531 7.736 17993 Z= 0.273 Chirality : 0.039 0.139 2071 Planarity : 0.004 0.048 2293 Dihedral : 4.226 54.057 1782 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.69 % Allowed : 17.27 % Favored : 80.04 % 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: 0.69 (0.21), residues: 1651 helix: 1.96 (0.20), residues: 691 sheet: 0.20 (0.28), residues: 372 loop : -1.20 (0.25), residues: 588 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 0.023 0.001 TYR B 242 ARG 0.002 0.000 ARG B 362 *********************** 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 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 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: 0.7715 (tmm) cc_final: 0.7220 (tmm) REVERT: A 157 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 313 CYS cc_start: 0.8151 (p) cc_final: 0.7923 (p) REVERT: A 915 MET cc_start: 0.7686 (mmt) cc_final: 0.7284 (mmt) REVERT: B 942 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7885 (mmtm) REVERT: B 1001 MET cc_start: 0.3336 (mmm) cc_final: 0.2314 (tpp) outliers start: 39 outliers final: 29 residues processed: 183 average time/residue: 0.2438 time to fit residues: 66.8337 Evaluate side-chains 170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 385 TYR Chi-restraints excluded: chain A residue 398 VAL 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 829 VAL 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 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 40.0000 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 884 HIS A1059 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13328 Z= 0.269 Angle : 0.575 8.103 17993 Z= 0.294 Chirality : 0.040 0.153 2071 Planarity : 0.004 0.048 2293 Dihedral : 4.373 53.931 1782 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.14 % Allowed : 16.30 % Favored : 79.56 % 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: 0.59 (0.21), residues: 1651 helix: 1.92 (0.20), residues: 685 sheet: 0.17 (0.28), residues: 372 loop : -1.30 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 778 HIS 0.006 0.001 HIS A 397 PHE 0.021 0.002 PHE A 869 TYR 0.028 0.002 TYR B 242 ARG 0.004 0.000 ARG B 747 *********************** 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 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7729 (tmm) cc_final: 0.7437 (tmm) REVERT: A 157 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 906 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8226 (mt0) REVERT: A 1013 GLN cc_start: 0.7188 (mt0) cc_final: 0.6520 (tp40) REVERT: B 438 ASN cc_start: 0.7709 (t0) cc_final: 0.7497 (t0) REVERT: B 942 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7929 (mmtm) REVERT: B 1001 MET cc_start: 0.3134 (mmm) cc_final: 0.2522 (mtp) outliers start: 60 outliers final: 41 residues processed: 195 average time/residue: 0.2437 time to fit residues: 71.7690 Evaluate side-chains 182 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 461 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 756 ILE 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 1096 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 249 HIS 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 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 488 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 746 THR 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 1059 HIS Chi-restraints excluded: chain B residue 1072 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 884 HIS A1059 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13328 Z= 0.347 Angle : 0.632 10.578 17993 Z= 0.324 Chirality : 0.042 0.177 2071 Planarity : 0.004 0.049 2293 Dihedral : 4.646 53.019 1782 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.56 % Allowed : 17.13 % Favored : 78.31 % 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: 0.32 (0.21), residues: 1651 helix: 1.68 (0.20), residues: 689 sheet: 0.09 (0.28), residues: 371 loop : -1.48 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 778 HIS 0.007 0.001 HIS A 397 PHE 0.023 0.002 PHE A 869 TYR 0.032 0.002 TYR B 242 ARG 0.002 0.000 ARG A1011 *********************** 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 214 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7808 (tmm) cc_final: 0.7485 (tmm) REVERT: A 157 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 274 ILE cc_start: 0.8666 (mp) cc_final: 0.8285 (mm) REVERT: A 1013 GLN cc_start: 0.7250 (mt0) cc_final: 0.6400 (tp40) REVERT: B 416 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.7774 (m) REVERT: B 438 ASN cc_start: 0.7717 (t0) cc_final: 0.7500 (t0) REVERT: B 572 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: B 942 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8054 (mmtm) REVERT: B 948 LEU cc_start: 0.7460 (mt) cc_final: 0.7222 (pp) REVERT: B 1001 MET cc_start: 0.2785 (mmm) cc_final: 0.2100 (mtp) outliers start: 66 outliers final: 49 residues processed: 198 average time/residue: 0.2444 time to fit residues: 72.5377 Evaluate side-chains 192 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 181 ASP 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 339 MET 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 416 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 SER 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 881 GLN 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 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 445 CYS Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 746 THR 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 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 54 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 161 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1059 HIS B1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13328 Z= 0.328 Angle : 0.638 10.328 17993 Z= 0.324 Chirality : 0.042 0.178 2071 Planarity : 0.004 0.051 2293 Dihedral : 4.695 52.798 1782 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.70 % Allowed : 18.09 % Favored : 77.21 % 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: 0.18 (0.21), residues: 1651 helix: 1.65 (0.20), residues: 685 sheet: -0.08 (0.28), residues: 376 loop : -1.59 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 778 HIS 0.006 0.001 HIS A 397 PHE 0.022 0.002 PHE A 869 TYR 0.030 0.002 TYR B 242 ARG 0.004 0.000 ARG A1011 *********************** 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 220 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7815 (tmm) cc_final: 0.7555 (tmm) REVERT: A 157 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 274 ILE cc_start: 0.8685 (mp) cc_final: 0.8303 (mm) REVERT: A 749 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: A 915 MET cc_start: 0.7530 (mmt) cc_final: 0.7242 (mmt) REVERT: A 920 MET cc_start: 0.7752 (tpt) cc_final: 0.7442 (tpp) REVERT: B 416 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7694 (m) REVERT: B 438 ASN cc_start: 0.7822 (t0) cc_final: 0.7533 (t0) REVERT: B 572 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: B 907 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.5898 (tp) REVERT: B 942 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8019 (mmtm) REVERT: B 1001 MET cc_start: 0.2928 (mmm) cc_final: 0.2282 (mtp) outliers start: 68 outliers final: 52 residues processed: 204 average time/residue: 0.2427 time to fit residues: 74.1114 Evaluate side-chains 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 230 VAL 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 339 MET 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 416 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 513 ILE 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 881 GLN 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 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 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 416 THR 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 572 GLU Chi-restraints excluded: chain B residue 746 THR 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 829 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 933 ILE Chi-restraints excluded: chain B residue 1059 HIS 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 155 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2121 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= 0.156 Angle : 0.567 9.173 17993 Z= 0.281 Chirality : 0.039 0.170 2071 Planarity : 0.004 0.053 2293 Dihedral : 4.286 53.128 1782 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.11 % Allowed : 19.89 % Favored : 77.00 % 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: 0.57 (0.21), residues: 1651 helix: 2.02 (0.20), residues: 686 sheet: 0.09 (0.29), residues: 356 loop : -1.38 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.006 0.001 HIS B 525 PHE 0.014 0.001 PHE A 869 TYR 0.017 0.001 TYR B 242 ARG 0.003 0.000 ARG A 299 *********************** 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 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7815 (tmm) cc_final: 0.7286 (tmm) REVERT: A 157 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 274 ILE cc_start: 0.8523 (mp) cc_final: 0.8177 (mm) REVERT: A 313 CYS cc_start: 0.8318 (p) cc_final: 0.8009 (p) REVERT: A 915 MET cc_start: 0.7546 (mmt) cc_final: 0.7238 (mmt) REVERT: A 920 MET cc_start: 0.7595 (tpt) cc_final: 0.7296 (tpp) REVERT: A 982 MET cc_start: 0.5604 (ppp) cc_final: 0.5350 (ppp) REVERT: B 438 ASN cc_start: 0.7830 (t0) cc_final: 0.7482 (t0) REVERT: B 942 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7910 (mmtm) REVERT: B 982 MET cc_start: 0.5941 (tpp) cc_final: 0.5253 (mtt) REVERT: B 1001 MET cc_start: 0.2896 (mmm) cc_final: 0.2202 (mtp) outliers start: 45 outliers final: 33 residues processed: 179 average time/residue: 0.2422 time to fit residues: 65.1410 Evaluate side-chains 170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 230 VAL 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 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 756 ILE Chi-restraints excluded: chain A residue 795 ASP 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 870 CYS Chi-restraints excluded: chain A residue 881 GLN 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 272 THR 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 746 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1059 HIS B 467 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13328 Z= 0.314 Angle : 0.658 10.069 17993 Z= 0.327 Chirality : 0.042 0.186 2071 Planarity : 0.004 0.053 2293 Dihedral : 4.573 53.520 1782 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.45 % Allowed : 19.34 % Favored : 77.21 % 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: 0.27 (0.21), residues: 1651 helix: 1.74 (0.20), residues: 687 sheet: 0.02 (0.28), residues: 371 loop : -1.63 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 778 HIS 0.006 0.001 HIS A 397 PHE 0.023 0.002 PHE A 869 TYR 0.029 0.002 TYR B 242 ARG 0.005 0.000 ARG A1011 *********************** 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 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7858 (tmm) cc_final: 0.7387 (tmm) REVERT: A 157 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 274 ILE cc_start: 0.8675 (mp) cc_final: 0.8310 (mm) REVERT: A 313 CYS cc_start: 0.8396 (p) cc_final: 0.8166 (p) REVERT: A 920 MET cc_start: 0.7705 (tpt) cc_final: 0.7416 (tpp) REVERT: A 1011 ARG cc_start: 0.7643 (mmm160) cc_final: 0.7415 (tpp-160) REVERT: A 1013 GLN cc_start: 0.7315 (mt0) cc_final: 0.6577 (tp40) REVERT: B 328 MET cc_start: 0.7861 (mmm) cc_final: 0.7273 (mpp) REVERT: B 438 ASN cc_start: 0.7801 (t0) cc_final: 0.7496 (t0) REVERT: B 508 MET cc_start: 0.8278 (ttp) cc_final: 0.8069 (tmm) REVERT: B 525 HIS cc_start: 0.7116 (t-90) cc_final: 0.6615 (t70) REVERT: B 942 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7922 (mmtm) REVERT: B 948 LEU cc_start: 0.7416 (mt) cc_final: 0.7148 (pp) REVERT: B 1001 MET cc_start: 0.2851 (mmm) cc_final: 0.2177 (mtp) outliers start: 50 outliers final: 42 residues processed: 178 average time/residue: 0.2546 time to fit residues: 69.0995 Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 230 VAL 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 398 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 524 SER 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 881 GLN 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 141 LEU Chi-restraints excluded: chain B residue 153 LEU 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 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 746 THR 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 870 CYS Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 1059 HIS 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 154 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 135 optimal weight: 0.0050 chunk 141 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13328 Z= 0.161 Angle : 0.591 11.200 17993 Z= 0.287 Chirality : 0.039 0.181 2071 Planarity : 0.004 0.054 2293 Dihedral : 4.205 53.332 1782 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 20.03 % Favored : 77.00 % 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: 0.61 (0.21), residues: 1651 helix: 2.04 (0.20), residues: 687 sheet: 0.17 (0.29), residues: 353 loop : -1.40 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.003 0.001 HIS B 577 PHE 0.014 0.001 PHE B 869 TYR 0.017 0.001 TYR B 242 ARG 0.005 0.000 ARG A1011 *********************** 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 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7874 (tmm) cc_final: 0.7634 (tmm) REVERT: A 274 ILE cc_start: 0.8510 (mp) cc_final: 0.8181 (mm) REVERT: A 280 PHE cc_start: 0.7298 (t80) cc_final: 0.7069 (t80) REVERT: A 313 CYS cc_start: 0.8330 (p) cc_final: 0.8047 (p) REVERT: A 915 MET cc_start: 0.7524 (mmt) cc_final: 0.7232 (mmt) REVERT: A 920 MET cc_start: 0.7571 (tpt) cc_final: 0.7285 (tpp) REVERT: A 982 MET cc_start: 0.5640 (ppp) cc_final: 0.5393 (ppp) REVERT: B 408 MET cc_start: 0.7272 (tmm) cc_final: 0.6941 (ttp) REVERT: B 438 ASN cc_start: 0.7815 (t0) cc_final: 0.7488 (t0) REVERT: B 942 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7927 (mmtm) REVERT: B 982 MET cc_start: 0.5898 (tpp) cc_final: 0.5244 (mtt) REVERT: B 1001 MET cc_start: 0.2776 (mmm) cc_final: 0.2091 (mtp) outliers start: 43 outliers final: 33 residues processed: 175 average time/residue: 0.2380 time to fit residues: 63.1359 Evaluate side-chains 170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 VAL Chi-restraints excluded: chain A residue 416 THR 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 756 ILE 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 881 GLN Chi-restraints excluded: chain A residue 897 LEU 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 272 THR 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 746 THR 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 1059 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 166 optimal weight: 40.0000 chunk 153 optimal weight: 0.0000 chunk 132 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13328 Z= 0.179 Angle : 0.599 10.471 17993 Z= 0.291 Chirality : 0.040 0.316 2071 Planarity : 0.004 0.053 2293 Dihedral : 4.153 54.376 1782 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.21 % Allowed : 20.44 % Favored : 77.35 % 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: 0.70 (0.21), residues: 1651 helix: 2.14 (0.20), residues: 685 sheet: 0.19 (0.29), residues: 357 loop : -1.35 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.003 0.001 HIS A 397 PHE 0.019 0.001 PHE A 231 TYR 0.018 0.001 TYR B 242 ARG 0.007 0.000 ARG B 747 ********************** 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 180 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7982 (tmm) cc_final: 0.7706 (tmm) REVERT: A 153 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7182 (pp) REVERT: A 274 ILE cc_start: 0.8527 (mp) cc_final: 0.8187 (mm) REVERT: A 280 PHE cc_start: 0.7299 (t80) cc_final: 0.7032 (t80) REVERT: A 313 CYS cc_start: 0.8367 (p) cc_final: 0.8102 (p) REVERT: A 425 MET cc_start: 0.8177 (mmt) cc_final: 0.7847 (mmm) REVERT: A 915 MET cc_start: 0.7521 (mmt) cc_final: 0.7233 (mmt) REVERT: A 920 MET cc_start: 0.7569 (tpt) cc_final: 0.7261 (tpp) REVERT: A 982 MET cc_start: 0.5658 (ppp) cc_final: 0.5394 (ppp) REVERT: B 438 ASN cc_start: 0.7836 (t0) cc_final: 0.7526 (t0) REVERT: B 525 HIS cc_start: 0.6994 (t-90) cc_final: 0.6518 (t70) REVERT: B 942 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7875 (mmtm) REVERT: B 1001 MET cc_start: 0.2848 (mmm) cc_final: 0.2153 (mtp) outliers start: 32 outliers final: 28 residues processed: 170 average time/residue: 0.2389 time to fit residues: 61.4591 Evaluate side-chains 171 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 398 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 756 ILE 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 881 GLN 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 272 THR 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 746 THR 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 1059 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.0010 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 0.0270 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.179583 restraints weight = 16967.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177125 restraints weight = 29268.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176236 restraints weight = 31145.955| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13328 Z= 0.152 Angle : 0.588 10.359 17993 Z= 0.284 Chirality : 0.040 0.259 2071 Planarity : 0.004 0.052 2293 Dihedral : 4.021 54.239 1782 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.07 % Allowed : 20.93 % Favored : 77.00 % 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: 0.83 (0.21), residues: 1651 helix: 2.23 (0.20), residues: 686 sheet: 0.25 (0.29), residues: 350 loop : -1.26 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.003 0.001 HIS B 577 PHE 0.014 0.001 PHE B 869 TYR 0.015 0.001 TYR B 99 ARG 0.004 0.000 ARG B 747 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.10 seconds wall clock time: 43 minutes 25.52 seconds (2605.52 seconds total)