Starting phenix.real_space_refine on Mon Dec 30 01:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9a_41105/12_2024/8t9a_41105.cif" } resolution = 3.17 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= 0.014 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 59 5.16 5 C 7468 2.51 5 N 2010 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11785 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8744 Classifications: {'peptide': 1114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 1073} Chain breaks: 4 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2998 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 364} Chain breaks: 4 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Time building chain proxies: 7.44, per 1000 atoms: 0.63 Number of scatterers: 11785 At special positions: 0 Unit cell: (89.112, 112.812, 146.94, 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 59 16.00 O 2248 8.00 N 2010 7.00 C 7468 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 33 sheets defined 6.8% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.578A pdb=" N SER A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1059 removed outlier: 3.807A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1090 through 1096 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.990A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1132 Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.752A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 removed outlier: 4.016A pdb=" N GLN B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.626A pdb=" N HIS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.296A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.797A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.993A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.734A pdb=" N ASP A 99 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 168 removed outlier: 5.834A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 201 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 263 removed outlier: 7.202A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 318 removed outlier: 5.422A pdb=" N TYR A 316 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 323 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 318 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AB2, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 379 removed outlier: 3.908A pdb=" N ILE A 390 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.669A pdb=" N SER A 690 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 692 " --> pdb=" O MET A 679 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET A 679 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 694 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 409 through 412 removed outlier: 4.064A pdb=" N GLY A 409 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.926A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.601A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 529 " --> pdb=" O TYR A 518 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.339A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 578 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 588 through 596 removed outlier: 3.780A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS A 600 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 615 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP A 625 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN A 617 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 623 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 637 through 643 removed outlier: 9.277A pdb=" N THR A 647 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 661 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 720 through 724 removed outlier: 6.505A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 811 through 820 removed outlier: 5.265A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 854 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.985A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 911 through 913 removed outlier: 6.687A pdb=" N GLY A 924 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 920 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 911 through 913 removed outlier: 6.687A pdb=" N GLY A 924 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 921 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.712A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 97 removed outlier: 6.384A pdb=" N GLY B 106 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER B 95 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 104 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP B 97 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 102 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.773A pdb=" N GLU B 147 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 167 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.335A pdb=" N SER B 189 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 255 through 257 removed outlier: 3.833A pdb=" N ALA B 257 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 277 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS B 280 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS B 287 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.719A pdb=" N LYS B 332 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 345 through 349 Processing sheet with id=AD6, first strand: chain 'B' and resid 420 through 425 removed outlier: 7.045A pdb=" N ALA B 436 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS B 424 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 434 " --> pdb=" O HIS B 424 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 891 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: 5.56 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3540 1.33 - 1.45: 2075 1.45 - 1.57: 6312 1.57 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 12014 Sorted by residual: bond pdb=" CA ARG A 134 " pdb=" CB ARG A 134 " ideal model delta sigma weight residual 1.539 1.346 0.193 4.88e-02 4.20e+02 1.56e+01 bond pdb=" CA TYR A 871 " pdb=" C TYR A 871 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.80e-02 3.09e+03 1.56e+01 bond pdb=" CA GLU A 896 " pdb=" C GLU A 896 " ideal model delta sigma weight residual 1.524 1.440 0.084 2.25e-02 1.98e+03 1.39e+01 bond pdb=" CG ARG A 134 " pdb=" CD ARG A 134 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.22e+00 bond pdb=" C VAL A 870 " pdb=" N TYR A 871 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.62e-02 3.81e+03 7.08e+00 ... (remaining 12009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 15585 2.17 - 4.34: 609 4.34 - 6.51: 67 6.51 - 8.68: 12 8.68 - 10.85: 4 Bond angle restraints: 16277 Sorted by residual: angle pdb=" N ILE A 884 " pdb=" CA ILE A 884 " pdb=" CB ILE A 884 " ideal model delta sigma weight residual 111.41 105.70 5.71 1.25e+00 6.40e-01 2.09e+01 angle pdb=" CA TYR A 871 " pdb=" C TYR A 871 " pdb=" N SER A 872 " ideal model delta sigma weight residual 118.27 125.17 -6.90 1.59e+00 3.96e-01 1.88e+01 angle pdb=" N GLY A 393 " pdb=" CA GLY A 393 " pdb=" C GLY A 393 " ideal model delta sigma weight residual 111.56 115.91 -4.35 1.01e+00 9.80e-01 1.86e+01 angle pdb=" N TRP A 411 " pdb=" CA TRP A 411 " pdb=" C TRP A 411 " ideal model delta sigma weight residual 108.25 113.05 -4.80 1.16e+00 7.43e-01 1.71e+01 angle pdb=" C ALA A 381 " pdb=" N PHE A 382 " pdb=" CA PHE A 382 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 ... (remaining 16272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6341 17.87 - 35.74: 698 35.74 - 53.61: 125 53.61 - 71.48: 27 71.48 - 89.35: 10 Dihedral angle restraints: 7201 sinusoidal: 2878 harmonic: 4323 Sorted by residual: dihedral pdb=" CA ASN B 59 " pdb=" C ASN B 59 " pdb=" N GLU B 60 " pdb=" CA GLU B 60 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLY A 274 " pdb=" C GLY A 274 " pdb=" N ASP A 275 " pdb=" CA ASP A 275 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR B 349 " pdb=" C TYR B 349 " pdb=" N GLU B 350 " pdb=" CA GLU B 350 " ideal model delta harmonic sigma weight residual -180.00 -157.29 -22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1342 0.059 - 0.117: 436 0.117 - 0.176: 67 0.176 - 0.235: 6 0.235 - 0.294: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CB ILE A 740 " pdb=" CA ILE A 740 " pdb=" CG1 ILE A 740 " pdb=" CG2 ILE A 740 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ARG A 134 " pdb=" N ARG A 134 " pdb=" C ARG A 134 " pdb=" CB ARG A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU B 79 " pdb=" CB LEU B 79 " pdb=" CD1 LEU B 79 " pdb=" CD2 LEU B 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1851 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 223 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 126 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 824 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 825 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 825 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 825 " -0.030 5.00e-02 4.00e+02 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 209 2.60 - 3.18: 10516 3.18 - 3.75: 17329 3.75 - 4.33: 25103 4.33 - 4.90: 42609 Nonbonded interactions: 95766 Sorted by model distance: nonbonded pdb=" OG1 THR B 107 " pdb=" OG1 THR B 111 " model vdw 2.029 3.040 nonbonded pdb=" O GLY A 227 " pdb=" OH TYR A 239 " model vdw 2.065 3.040 nonbonded pdb=" OG SER B 95 " pdb=" OG1 THR B 423 " model vdw 2.081 3.040 nonbonded pdb=" O ASN A 617 " pdb=" N GLY A 621 " model vdw 2.132 3.120 nonbonded pdb=" O ILE A 310 " pdb=" OG SER A 326 " model vdw 2.140 3.040 ... (remaining 95761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.90 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 32.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.011 0.193 12014 Z= 0.762 Angle : 0.980 10.852 16277 Z= 0.540 Chirality : 0.056 0.294 1854 Planarity : 0.006 0.077 2094 Dihedral : 15.501 89.350 4417 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 0.61 % Allowed : 12.80 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -5.00 (0.17), residues: 1476 helix: -3.44 (0.35), residues: 104 sheet: -2.58 (0.19), residues: 620 loop : -4.03 (0.16), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 207 HIS 0.009 0.002 HIS B 237 PHE 0.034 0.003 PHE A 733 TYR 0.029 0.003 TYR B 349 ARG 0.007 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7866 (p0) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.2480 time to fit residues: 32.3074 Evaluate side-chains 58 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 323 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 355 ASN A 759 GLN A 803 HIS A 907 ASN A 950 ASN A1034 ASN A1077 HIS B 99 ASN B 224 HIS B 359 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12014 Z= 0.319 Angle : 0.702 7.528 16277 Z= 0.369 Chirality : 0.047 0.226 1854 Planarity : 0.005 0.063 2094 Dihedral : 5.830 33.127 1616 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.83 % Allowed : 15.70 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -4.00 (0.19), residues: 1476 helix: -2.53 (0.43), residues: 104 sheet: -1.88 (0.19), residues: 636 loop : -3.43 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 207 HIS 0.008 0.001 HIS A 522 PHE 0.016 0.002 PHE A1030 TYR 0.020 0.002 TYR B 410 ARG 0.005 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 954 MET cc_start: 0.7794 (mmm) cc_final: 0.7564 (mmp) REVERT: B 302 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8650 (tp) outliers start: 24 outliers final: 8 residues processed: 74 average time/residue: 0.2410 time to fit residues: 27.2378 Evaluate side-chains 58 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 overall best weight: 2.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12014 Z= 0.224 Angle : 0.626 7.250 16277 Z= 0.328 Chirality : 0.046 0.194 1854 Planarity : 0.004 0.058 2094 Dihedral : 5.238 25.895 1613 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.06 % Allowed : 16.54 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.20), residues: 1476 helix: -1.86 (0.46), residues: 104 sheet: -1.58 (0.20), residues: 629 loop : -3.00 (0.19), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.004 0.001 HIS B 424 PHE 0.013 0.001 PHE A1030 TYR 0.012 0.001 TYR A 613 ARG 0.004 0.000 ARG A 947 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 1.259 Fit side-chains REVERT: A 130 MET cc_start: 0.7823 (ppp) cc_final: 0.7108 (ppp) REVERT: B 302 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8606 (tp) outliers start: 27 outliers final: 9 residues processed: 82 average time/residue: 0.2249 time to fit residues: 29.1036 Evaluate side-chains 62 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 302 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 chunk 135 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 overall best weight: 3.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12014 Z= 0.285 Angle : 0.647 7.270 16277 Z= 0.335 Chirality : 0.045 0.183 1854 Planarity : 0.004 0.058 2094 Dihedral : 5.045 23.042 1611 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.82 % Allowed : 17.38 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.20), residues: 1476 helix: -1.55 (0.46), residues: 106 sheet: -1.48 (0.20), residues: 632 loop : -2.80 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.004 0.001 HIS B 424 PHE 0.013 0.001 PHE A1030 TYR 0.015 0.001 TYR B 329 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7880 (ppp) cc_final: 0.7274 (ppp) REVERT: B 302 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 323 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8331 (p0) outliers start: 37 outliers final: 21 residues processed: 86 average time/residue: 0.2138 time to fit residues: 29.5565 Evaluate side-chains 71 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 453 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 0.0470 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12014 Z= 0.289 Angle : 0.644 11.664 16277 Z= 0.331 Chirality : 0.045 0.219 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.959 23.476 1611 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.59 % Allowed : 18.22 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.20), residues: 1476 helix: -1.27 (0.47), residues: 106 sheet: -1.30 (0.21), residues: 617 loop : -2.71 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 186 HIS 0.004 0.001 HIS A 711 PHE 0.013 0.001 PHE A1030 TYR 0.013 0.001 TYR A 613 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 49 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: A 1120 MET cc_start: 0.5291 (tmm) cc_final: 0.4965 (tmm) REVERT: B 154 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8691 (mm) REVERT: B 302 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8576 (tp) outliers start: 34 outliers final: 22 residues processed: 80 average time/residue: 0.2224 time to fit residues: 27.4152 Evaluate side-chains 70 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12014 Z= 0.302 Angle : 0.650 10.808 16277 Z= 0.333 Chirality : 0.045 0.182 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.929 23.922 1611 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.20 % Allowed : 18.60 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.20), residues: 1476 helix: -1.14 (0.47), residues: 108 sheet: -1.15 (0.21), residues: 601 loop : -2.72 (0.19), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1073 HIS 0.004 0.001 HIS A 711 PHE 0.012 0.001 PHE A1030 TYR 0.013 0.001 TYR A 613 ARG 0.011 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 47 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5859 (tt0) REVERT: B 154 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8695 (mm) REVERT: B 302 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8555 (tp) outliers start: 42 outliers final: 27 residues processed: 84 average time/residue: 0.2610 time to fit residues: 34.2980 Evaluate side-chains 76 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 46 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 12014 Z= 0.438 Angle : 0.727 10.204 16277 Z= 0.370 Chirality : 0.046 0.181 1854 Planarity : 0.004 0.059 2094 Dihedral : 5.217 25.942 1611 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.20 % Allowed : 19.36 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.20), residues: 1476 helix: -1.41 (0.46), residues: 114 sheet: -1.19 (0.21), residues: 601 loop : -2.73 (0.19), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 192 HIS 0.007 0.001 HIS A 711 PHE 0.015 0.002 PHE A 807 TYR 0.015 0.002 TYR A 613 ARG 0.009 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 44 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5949 (tt0) REVERT: A 1120 MET cc_start: 0.5584 (tmm) cc_final: 0.5136 (tmm) REVERT: B 154 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 302 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8724 (tp) outliers start: 42 outliers final: 29 residues processed: 81 average time/residue: 0.2273 time to fit residues: 28.5359 Evaluate side-chains 72 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 50.0000 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 30.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12014 Z= 0.155 Angle : 0.626 10.834 16277 Z= 0.317 Chirality : 0.046 0.166 1854 Planarity : 0.004 0.057 2094 Dihedral : 4.720 23.119 1611 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.98 % Allowed : 21.11 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.21), residues: 1476 helix: -0.96 (0.48), residues: 113 sheet: -1.05 (0.21), residues: 608 loop : -2.51 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 893 HIS 0.004 0.001 HIS B 424 PHE 0.013 0.001 PHE A1030 TYR 0.010 0.001 TYR A 613 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 1120 MET cc_start: 0.5357 (tmm) cc_final: 0.5120 (tmm) REVERT: B 302 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 310 ARG cc_start: 0.5255 (mmt180) cc_final: 0.4952 (mmp80) outliers start: 26 outliers final: 19 residues processed: 69 average time/residue: 0.2447 time to fit residues: 25.9593 Evaluate side-chains 64 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 overall best weight: 3.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12014 Z= 0.291 Angle : 0.662 11.897 16277 Z= 0.333 Chirality : 0.045 0.168 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.798 23.925 1611 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.13 % Allowed : 21.27 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.21), residues: 1476 helix: -0.93 (0.48), residues: 114 sheet: -1.04 (0.21), residues: 597 loop : -2.52 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.005 0.001 HIS A 711 PHE 0.013 0.001 PHE A1030 TYR 0.012 0.001 TYR A 613 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 1.383 Fit side-chains REVERT: A 1120 MET cc_start: 0.5576 (tmm) cc_final: 0.5309 (tmm) REVERT: B 302 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8648 (tp) outliers start: 28 outliers final: 21 residues processed: 69 average time/residue: 0.2412 time to fit residues: 25.6852 Evaluate side-chains 67 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 93 optimal weight: 0.0030 chunk 125 optimal weight: 9.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12014 Z= 0.181 Angle : 0.643 11.657 16277 Z= 0.320 Chirality : 0.046 0.177 1854 Planarity : 0.004 0.056 2094 Dihedral : 4.635 22.955 1611 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.83 % Allowed : 21.80 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1476 helix: -0.76 (0.49), residues: 114 sheet: -0.94 (0.21), residues: 599 loop : -2.45 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 893 HIS 0.003 0.001 HIS B 424 PHE 0.011 0.001 PHE A1030 TYR 0.011 0.001 TYR A 613 ARG 0.006 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.438 Fit side-chains REVERT: A 1120 MET cc_start: 0.5521 (tmm) cc_final: 0.5281 (tmm) REVERT: B 154 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8535 (mm) REVERT: B 302 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8475 (tp) outliers start: 24 outliers final: 20 residues processed: 67 average time/residue: 0.2481 time to fit residues: 26.6540 Evaluate side-chains 68 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.0000 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.076045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049596 restraints weight = 48084.849| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.10 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12014 Z= 0.147 Angle : 0.623 11.387 16277 Z= 0.309 Chirality : 0.045 0.164 1854 Planarity : 0.004 0.057 2094 Dihedral : 4.347 20.918 1611 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.52 % Allowed : 22.18 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1476 helix: 0.03 (0.53), residues: 107 sheet: -0.92 (0.21), residues: 606 loop : -2.31 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 893 HIS 0.003 0.001 HIS B 424 PHE 0.035 0.001 PHE A 382 TYR 0.009 0.001 TYR A 613 ARG 0.006 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.19 seconds wall clock time: 42 minutes 50.45 seconds (2570.45 seconds total)