Starting phenix.real_space_refine on Thu Jul 2 15:31:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/07_2026/8dk3_27482.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 5414 2.51 5 N 1597 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3530 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 12, 'TRANS': 442} Chain breaks: 2 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3494 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 12, 'TRANS': 437} Chain breaks: 2 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 751 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.59, per 1000 atoms: 0.18 Number of scatterers: 8905 At special positions: 0 Unit cell: (89.1, 111.1, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 P 58 15.00 Mg 2 11.99 O 1811 8.00 N 1597 7.00 C 5414 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: 0.65 Conformation dependent library (CDL) restraints added in 174.8 milliseconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 46.0% alpha, 18.5% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.770A pdb=" N LEU A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.536A pdb=" N THR A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.528A pdb=" N TYR A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.609A pdb=" N ALA A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.883A pdb=" N MET A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 200 through 208 Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.926A pdb=" N ILE A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 857 through 881 Processing helix chain 'A' and resid 902 through 915 removed outlier: 4.495A pdb=" N THR A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 944 removed outlier: 3.841A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 955 Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 985 through 1005 removed outlier: 3.719A pdb=" N LYS A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 991 " --> pdb=" O GLY A 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'A' and resid 1028 through 1043 removed outlier: 3.649A pdb=" N ALA A1032 " --> pdb=" O SER A1028 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 removed outlier: 3.684A pdb=" N ARG A1059 " --> pdb=" O MET A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1088 removed outlier: 3.645A pdb=" N HIS A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.557A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.655A pdb=" N THR B 71 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.648A pdb=" N TYR B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.875A pdb=" N LEU B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 200 through 208 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.768A pdb=" N ILE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 858 through 882 removed outlier: 3.733A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 918 removed outlier: 3.986A pdb=" N ARG B 905 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 918 " --> pdb=" O LEU B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 944 removed outlier: 4.384A pdb=" N LEU B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 955 removed outlier: 4.047A pdb=" N LEU B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 958 No H-bonds generated for 'chain 'B' and resid 956 through 958' Processing helix chain 'B' and resid 985 through 1005 removed outlier: 3.760A pdb=" N LYS B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 991 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1043 removed outlier: 3.613A pdb=" N PHE B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1062 removed outlier: 3.941A pdb=" N HIS B1060 " --> pdb=" O ARG B1056 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 425 Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.875A pdb=" N GLY A 28 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 15 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU A 115 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 17 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 111 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 109 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP A 23 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N VAL A 107 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 116 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 140 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1018 through 1021 removed outlier: 3.747A pdb=" N THR A 39 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A1074 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 898 removed outlier: 4.160A pdb=" N GLU A 976 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP A 968 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 974 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.164A pdb=" N GLY B 28 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 21 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS B 30 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU B 19 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA B 32 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER B 17 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 113 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE B 18 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 111 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 20 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 109 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN B 22 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 107 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 125 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 144 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 128 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1017 through 1019 removed outlier: 4.067A pdb=" N ALA B1065 " --> pdb=" O LEU B1080 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 890 through 898 removed outlier: 3.847A pdb=" N GLU B 976 " --> pdb=" O VAL B 966 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP B 968 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 974 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 460 through 472 removed outlier: 7.253A pdb=" N GLU C 464 " --> pdb=" O TYR C 484 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 484 " --> pdb=" O GLU C 464 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP C 472 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2961 1.36 - 1.50: 2895 1.50 - 1.65: 3283 1.65 - 1.80: 22 1.80 - 1.94: 16 Bond restraints: 9177 Sorted by residual: bond pdb=" C3' DT P 13 " pdb=" C2' DT P 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT P 8 " pdb=" C2' DT P 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT P 21 " pdb=" C2' DT P 21 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.17e+00 bond pdb=" C3' DT P 23 " pdb=" C2' DT P 23 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.07e+00 bond pdb=" C3' DT P 5 " pdb=" C2' DT P 5 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.75e+00 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 11893 1.26 - 2.52: 623 2.52 - 3.78: 115 3.78 - 5.04: 11 5.04 - 6.30: 3 Bond angle restraints: 12645 Sorted by residual: angle pdb=" C GLU C 475 " pdb=" CA GLU C 475 " pdb=" CB GLU C 475 " ideal model delta sigma weight residual 116.54 110.24 6.30 1.15e+00 7.56e-01 3.00e+01 angle pdb=" N3 DT P 24 " pdb=" C4 DT P 24 " pdb=" O4 DT P 24 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT P 14 " pdb=" C4 DT P 14 " pdb=" O4 DT P 14 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 ... (remaining 12640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.79: 4871 22.79 - 45.58: 361 45.58 - 68.38: 133 68.38 - 91.17: 1 91.17 - 113.96: 1 Dihedral angle restraints: 5367 sinusoidal: 2520 harmonic: 2847 Sorted by residual: dihedral pdb=" O1A AGS A1201 " pdb=" O3A AGS A1201 " pdb=" PA AGS A1201 " pdb=" PB AGS A1201 " ideal model delta sinusoidal sigma weight residual -67.73 46.23 -113.96 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA GLN A 887 " pdb=" C GLN A 887 " pdb=" N PRO A 888 " pdb=" CA PRO A 888 " ideal model delta harmonic sigma weight residual 180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB ARG B 78 " pdb=" CG ARG B 78 " pdb=" CD ARG B 78 " pdb=" NE ARG B 78 " ideal model delta sinusoidal sigma weight residual -60.00 -118.84 58.84 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 669 0.026 - 0.053: 454 0.053 - 0.079: 160 0.079 - 0.105: 101 0.105 - 0.132: 36 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA PRO B 888 " pdb=" N PRO B 888 " pdb=" C PRO B 888 " pdb=" CB PRO B 888 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" PA AGS A1201 " pdb=" O2A AGS A1201 " pdb=" O3A AGS A1201 " pdb=" O5' AGS A1201 " both_signs ideal model delta sigma weight residual True 3.18 3.05 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1417 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 887 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 888 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 888 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 888 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 179 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 180 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 35 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO B 36 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.019 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 40 2.48 - 3.08: 5910 3.08 - 3.69: 12225 3.69 - 4.29: 17153 4.29 - 4.90: 28481 Nonbonded interactions: 63809 Sorted by model distance: nonbonded pdb=" OG1 THR B 50 " pdb="MG MG B1202 " model vdw 1.869 2.170 nonbonded pdb=" O2B AGS A1201 " pdb="MG MG A1202 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR A 50 " pdb="MG MG A1202 " model vdw 1.982 2.170 nonbonded pdb=" O2B AGS A1201 " pdb=" O2G AGS A1201 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 429 " pdb=" OE1 GLU C 432 " model vdw 2.159 3.040 ... (remaining 63804 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 10 through 242 or resid 857 through 1083 or resid 1201 thr \ ough 1202)) selection = (chain 'B' and (resid 10 through 917 or resid 929 through 1202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.006 0.033 9177 Z= 0.359 Angle : 0.635 6.299 12645 Z= 0.454 Chirality : 0.044 0.132 1420 Planarity : 0.004 0.046 1447 Dihedral : 16.338 113.958 3533 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.85 % Allowed : 6.33 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 985 helix: 1.71 (0.27), residues: 394 sheet: -0.59 (0.36), residues: 204 loop : -1.73 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1059 TYR 0.012 0.001 TYR B 862 PHE 0.013 0.001 PHE B 187 TRP 0.008 0.001 TRP A 128 HIS 0.005 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.36 ( 9177) covalent geometry : angle 0.63475 / 0.45 (12645) hydrogen bonds : bond 0.20241 / 13.59 ( 411) hydrogen bonds : angle 6.21928 / 4.26 ( 1154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8663 (p-80) cc_final: 0.8447 (p-80) REVERT: C 409 ASP cc_start: 0.8641 (t0) cc_final: 0.8061 (t0) REVERT: C 476 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8688 (mm110) REVERT: C 495 ILE cc_start: 0.9033 (tp) cc_final: 0.8742 (pt) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.0953 time to fit residues: 6.6636 Evaluate side-chains 36 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1019 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 103 GLN A1022 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044775 restraints weight = 30479.256| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.32 r_work: 0.2615 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9177 Z= 0.169 Angle : 0.577 6.996 12645 Z= 0.322 Chirality : 0.039 0.146 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.326 119.537 1729 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.09 % Allowed : 8.39 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 985 helix: 1.62 (0.27), residues: 402 sheet: -0.33 (0.36), residues: 205 loop : -1.82 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 883 TYR 0.013 0.001 TYR B 862 PHE 0.008 0.001 PHE B 886 TRP 0.007 0.001 TRP A 128 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 9177) covalent geometry : angle 0.57689 / 0.32 (12645) hydrogen bonds : bond 0.05747 / 3.83 ( 411) hydrogen bonds : angle 4.67180 / 3.27 ( 1154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8555 (p-80) cc_final: 0.8320 (p-80) REVERT: C 409 ASP cc_start: 0.8542 (t0) cc_final: 0.7829 (t0) REVERT: C 495 ILE cc_start: 0.8999 (tp) cc_final: 0.8711 (pt) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.0870 time to fit residues: 5.9659 Evaluate side-chains 37 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044568 restraints weight = 30472.037| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.35 r_work: 0.2622 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9177 Z= 0.153 Angle : 0.532 9.629 12645 Z= 0.302 Chirality : 0.039 0.140 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.329 115.582 1727 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.46 % Allowed : 9.85 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.27), residues: 985 helix: 1.66 (0.27), residues: 402 sheet: -0.34 (0.35), residues: 205 loop : -1.83 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 883 TYR 0.014 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 9177) covalent geometry : angle 0.53169 / 0.30 (12645) hydrogen bonds : bond 0.05011 / 3.37 ( 411) hydrogen bonds : angle 4.30146 / 3.00 ( 1154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.332 Fit side-chains REVERT: A 901 HIS cc_start: 0.8501 (p-80) cc_final: 0.8267 (p-80) REVERT: C 409 ASP cc_start: 0.8476 (t0) cc_final: 0.7690 (t0) REVERT: C 495 ILE cc_start: 0.9016 (tp) cc_final: 0.8775 (pt) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.0800 time to fit residues: 5.9796 Evaluate side-chains 39 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.065425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.045601 restraints weight = 30485.033| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.31 r_work: 0.2655 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9177 Z= 0.116 Angle : 0.499 6.929 12645 Z= 0.284 Chirality : 0.038 0.146 1420 Planarity : 0.003 0.042 1447 Dihedral : 19.332 116.433 1727 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.09 % Allowed : 10.95 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 985 helix: 1.79 (0.27), residues: 400 sheet: -0.41 (0.35), residues: 208 loop : -1.78 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 410 TYR 0.014 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 9177) covalent geometry : angle 0.49889 / 0.28 (12645) hydrogen bonds : bond 0.04064 / 2.73 ( 411) hydrogen bonds : angle 4.03224 / 2.82 ( 1154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8509 (p-80) cc_final: 0.8276 (p-80) REVERT: C 409 ASP cc_start: 0.8485 (t0) cc_final: 0.7706 (t0) REVERT: C 465 ARG cc_start: 0.8462 (mmt180) cc_final: 0.7881 (mmt180) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.0960 time to fit residues: 6.1915 Evaluate side-chains 40 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 493 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.044505 restraints weight = 30607.638| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.31 r_work: 0.2619 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9177 Z= 0.179 Angle : 0.539 6.571 12645 Z= 0.301 Chirality : 0.039 0.134 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.462 114.631 1727 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.95 % Allowed : 11.19 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 985 helix: 1.75 (0.27), residues: 400 sheet: -0.38 (0.35), residues: 205 loop : -1.84 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.015 0.001 TYR B 862 PHE 0.008 0.001 PHE B 187 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9177) covalent geometry : angle 0.53894 / 0.30 (12645) hydrogen bonds : bond 0.05035 / 3.39 ( 411) hydrogen bonds : angle 4.11499 / 2.88 ( 1154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8529 (p-80) cc_final: 0.8300 (p-80) REVERT: B 974 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9147 (tt) REVERT: C 409 ASP cc_start: 0.8569 (t0) cc_final: 0.7779 (t0) REVERT: C 465 ARG cc_start: 0.8457 (mmt180) cc_final: 0.7844 (mmt180) outliers start: 16 outliers final: 10 residues processed: 50 average time/residue: 0.0792 time to fit residues: 5.9710 Evaluate side-chains 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044598 restraints weight = 30427.674| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.30 r_work: 0.2620 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9177 Z= 0.165 Angle : 0.529 5.959 12645 Z= 0.297 Chirality : 0.038 0.137 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.500 114.397 1727 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.95 % Allowed : 11.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.27), residues: 985 helix: 1.70 (0.27), residues: 400 sheet: -0.43 (0.35), residues: 205 loop : -1.87 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 410 TYR 0.014 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 9177) covalent geometry : angle 0.52934 / 0.30 (12645) hydrogen bonds : bond 0.04785 / 3.22 ( 411) hydrogen bonds : angle 4.07145 / 2.86 ( 1154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8491 (p-80) cc_final: 0.8258 (p-80) REVERT: B 974 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 409 ASP cc_start: 0.8586 (t0) cc_final: 0.7799 (t0) REVERT: C 465 ARG cc_start: 0.8431 (mmt180) cc_final: 0.7808 (mmt180) outliers start: 16 outliers final: 10 residues processed: 50 average time/residue: 0.0882 time to fit residues: 6.6404 Evaluate side-chains 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.044474 restraints weight = 30208.187| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.28 r_work: 0.2622 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9177 Z= 0.181 Angle : 0.546 5.730 12645 Z= 0.304 Chirality : 0.039 0.134 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.562 113.729 1727 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.70 % Allowed : 12.29 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.27), residues: 985 helix: 1.66 (0.27), residues: 400 sheet: -0.46 (0.35), residues: 205 loop : -1.91 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.014 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9177) covalent geometry : angle 0.54555 / 0.30 (12645) hydrogen bonds : bond 0.05120 / 3.44 ( 411) hydrogen bonds : angle 4.11567 / 2.89 ( 1154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 901 HIS cc_start: 0.8501 (p-80) cc_final: 0.8267 (p-80) REVERT: B 974 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9189 (tt) REVERT: C 409 ASP cc_start: 0.8600 (t0) cc_final: 0.7804 (t0) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.0790 time to fit residues: 5.8770 Evaluate side-chains 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044448 restraints weight = 30501.608| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.32 r_work: 0.2621 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9177 Z= 0.151 Angle : 0.532 10.223 12645 Z= 0.295 Chirality : 0.038 0.139 1420 Planarity : 0.003 0.044 1447 Dihedral : 19.564 113.785 1727 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.70 % Allowed : 12.53 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.27), residues: 985 helix: 1.73 (0.27), residues: 399 sheet: -0.52 (0.35), residues: 208 loop : -1.87 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 426 TYR 0.014 0.001 TYR B 862 PHE 0.007 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9177) covalent geometry : angle 0.53234 / 0.30 (12645) hydrogen bonds : bond 0.04677 / 3.14 ( 411) hydrogen bonds : angle 4.03022 / 2.83 ( 1154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8498 (p-80) cc_final: 0.8284 (p-80) REVERT: B 974 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9177 (tt) REVERT: C 409 ASP cc_start: 0.8588 (t0) cc_final: 0.7793 (t0) REVERT: C 465 ARG cc_start: 0.8438 (mmt180) cc_final: 0.7826 (mmt180) outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.0917 time to fit residues: 6.6806 Evaluate side-chains 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.063899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.044051 restraints weight = 30221.306| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.29 r_work: 0.2621 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9177 Z= 0.182 Angle : 0.555 9.531 12645 Z= 0.305 Chirality : 0.039 0.136 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.637 113.549 1727 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.70 % Allowed : 12.90 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.27), residues: 985 helix: 1.65 (0.27), residues: 400 sheet: -0.49 (0.35), residues: 205 loop : -1.94 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.014 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 9177) covalent geometry : angle 0.55477 / 0.31 (12645) hydrogen bonds : bond 0.05143 / 3.45 ( 411) hydrogen bonds : angle 4.10403 / 2.88 ( 1154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 901 HIS cc_start: 0.8517 (p-80) cc_final: 0.8301 (p-80) REVERT: B 974 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9181 (tt) REVERT: C 409 ASP cc_start: 0.8599 (t0) cc_final: 0.7794 (t0) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.0816 time to fit residues: 6.0812 Evaluate side-chains 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045077 restraints weight = 30081.334| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.27 r_work: 0.2650 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9177 Z= 0.121 Angle : 0.507 6.893 12645 Z= 0.284 Chirality : 0.037 0.144 1420 Planarity : 0.003 0.043 1447 Dihedral : 19.597 112.879 1727 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.46 % Allowed : 13.02 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 985 helix: 1.80 (0.27), residues: 399 sheet: -0.49 (0.35), residues: 208 loop : -1.85 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 426 TYR 0.014 0.001 TYR B 862 PHE 0.007 0.001 PHE B 886 TRP 0.008 0.001 TRP B 128 HIS 0.002 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9177) covalent geometry : angle 0.50686 / 0.28 (12645) hydrogen bonds : bond 0.04127 / 2.78 ( 411) hydrogen bonds : angle 3.91408 / 2.75 ( 1154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 974 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9201 (tt) REVERT: C 409 ASP cc_start: 0.8574 (t0) cc_final: 0.7771 (t0) REVERT: C 465 ARG cc_start: 0.8411 (mmt180) cc_final: 0.7783 (mmt180) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.0914 time to fit residues: 6.4010 Evaluate side-chains 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.043879 restraints weight = 30019.087| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.27 r_work: 0.2620 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9177 Z= 0.216 Angle : 0.571 6.883 12645 Z= 0.314 Chirality : 0.040 0.132 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.698 113.203 1727 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.46 % Allowed : 12.90 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.27), residues: 985 helix: 1.68 (0.27), residues: 400 sheet: -0.46 (0.35), residues: 203 loop : -1.94 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.014 0.001 TYR B 862 PHE 0.009 0.001 PHE B 187 TRP 0.009 0.001 TRP B 128 HIS 0.009 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 9177) covalent geometry : angle 0.57050 / 0.31 (12645) hydrogen bonds : bond 0.05309 / 3.56 ( 411) hydrogen bonds : angle 4.11229 / 2.89 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.29 seconds wall clock time: 33 minutes 4.16 seconds (1984.16 seconds total)