Starting phenix.real_space_refine on Fri Sep 11 11:18:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_2026/8dk3_27482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dk3_27482/09_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-2.2.1-6174/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: 2.04, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 298.9 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: 0.90 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: 1.50 Time building geometry restraints manager: 1.13 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- 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 : 0.636 6.299 12645 Z= 0.455 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 0.63592 / 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 : 0.369 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: 0.1148 time to fit residues: 7.9457 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 : 0.331 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.064410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044456 restraints weight = 30619.234| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.35 r_work: 0.2613 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9177 Z= 0.168 Angle : 0.582 7.023 12645 Z= 0.325 Chirality : 0.039 0.148 1420 Planarity : 0.004 0.047 1447 Dihedral : 19.322 119.525 1729 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.97 % Allowed : 8.64 % Favored : 90.39 % 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: 1.61 (0.27), residues: 402 sheet: -0.35 (0.35), residues: 206 loop : -1.81 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 883 TYR 0.013 0.001 TYR B 862 PHE 0.008 0.001 PHE A 221 TRP 0.007 0.001 TRP A 128 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 9177) covalent geometry : angle 0.58238 / 0.33 (12645) hydrogen bonds : bond 0.05798 / 3.86 ( 411) hydrogen bonds : angle 4.68889 / 3.28 ( 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 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8509 (p-80) cc_final: 0.8273 (p-80) REVERT: C 409 ASP cc_start: 0.8552 (t0) cc_final: 0.7832 (t0) REVERT: C 495 ILE cc_start: 0.9016 (tp) cc_final: 0.8731 (pt) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.0798 time to fit residues: 5.4271 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 : 0.294 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.064786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.044812 restraints weight = 30486.561| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.35 r_work: 0.2631 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9177 Z= 0.138 Angle : 0.524 9.540 12645 Z= 0.298 Chirality : 0.038 0.144 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.286 116.084 1727 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.34 % Allowed : 9.73 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.27), residues: 985 helix: 1.71 (0.27), residues: 401 sheet: -0.32 (0.35), residues: 205 loop : -1.81 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 883 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 0.00286 / 0.14 ( 9177) covalent geometry : angle 0.52418 / 0.30 (12645) hydrogen bonds : bond 0.04809 / 3.23 ( 411) hydrogen bonds : angle 4.29476 / 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.353 Fit side-chains REVERT: A 901 HIS cc_start: 0.8530 (p-80) cc_final: 0.8299 (p-80) REVERT: C 409 ASP cc_start: 0.8479 (t0) cc_final: 0.7705 (t0) REVERT: C 495 ILE cc_start: 0.8997 (tp) cc_final: 0.8745 (pt) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.0708 time to fit residues: 5.2197 Evaluate side-chains 38 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.064997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.045043 restraints weight = 30808.345| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.37 r_work: 0.2645 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9177 Z= 0.130 Angle : 0.507 6.722 12645 Z= 0.288 Chirality : 0.038 0.143 1420 Planarity : 0.003 0.043 1447 Dihedral : 19.333 116.867 1727 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % 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: -0.02 (0.27), residues: 985 helix: 1.75 (0.27), residues: 401 sheet: -0.33 (0.35), residues: 205 loop : -1.81 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.00267 / 0.13 ( 9177) covalent geometry : angle 0.50728 / 0.29 (12645) hydrogen bonds : bond 0.04354 / 2.93 ( 411) hydrogen bonds : angle 4.07939 / 2.86 ( 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8512 (p-80) cc_final: 0.8282 (p-80) REVERT: C 409 ASP cc_start: 0.8496 (t0) cc_final: 0.7718 (t0) REVERT: C 465 ARG cc_start: 0.8467 (mmt180) cc_final: 0.7878 (mmt180) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.0926 time to fit residues: 6.2668 Evaluate side-chains 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 145 LEU 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 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: 0.5980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 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: 0.9980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.064100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044255 restraints weight = 30639.274| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.31 r_work: 0.2615 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 9177 Z= 0.197 Angle : 0.556 6.498 12645 Z= 0.308 Chirality : 0.039 0.132 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.457 114.834 1727 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.95 % Allowed : 11.07 % Favored : 86.98 % 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: -0.15 (0.27), residues: 985 helix: 1.68 (0.27), residues: 400 sheet: -0.43 (0.35), residues: 205 loop : -1.89 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.015 0.001 TYR B 862 PHE 0.009 0.001 PHE B 187 TRP 0.009 0.001 TRP C 497 HIS 0.005 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 9177) covalent geometry : angle 0.55561 / 0.31 (12645) hydrogen bonds : bond 0.05293 / 3.56 ( 411) hydrogen bonds : angle 4.18456 / 2.94 ( 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 : 0.212 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8528 (p-80) cc_final: 0.8299 (p-80) REVERT: B 974 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9161 (tt) REVERT: C 409 ASP cc_start: 0.8580 (t0) cc_final: 0.7794 (t0) REVERT: C 465 ARG cc_start: 0.8426 (mmt180) cc_final: 0.7770 (mmt180) outliers start: 16 outliers final: 10 residues processed: 50 average time/residue: 0.0834 time to fit residues: 6.2108 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 : 0.319 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.063853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043762 restraints weight = 31143.576| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.39 r_work: 0.2605 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1407 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= 0.191 Angle : 0.561 9.670 12645 Z= 0.310 Chirality : 0.039 0.135 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.495 114.558 1727 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.82 % Allowed : 12.04 % Favored : 86.13 % 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: -0.26 (0.27), residues: 985 helix: 1.58 (0.27), residues: 400 sheet: -0.50 (0.35), residues: 205 loop : -1.95 (0.29), residues: 380 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 0.008 0.001 PHE B 187 TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 9177) covalent geometry : angle 0.56139 / 0.31 (12645) hydrogen bonds : bond 0.05180 / 3.48 ( 411) hydrogen bonds : angle 4.17753 / 2.94 ( 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 48 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8507 (p-80) cc_final: 0.8275 (p-80) REVERT: B 974 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9179 (tt) REVERT: C 409 ASP cc_start: 0.8599 (t0) cc_final: 0.7821 (t0) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 0.0745 time to fit residues: 5.7001 Evaluate side-chains 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 3.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 91 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.064717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.044830 restraints weight = 30461.528| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.31 r_work: 0.2633 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9177 Z= 0.135 Angle : 0.514 6.058 12645 Z= 0.289 Chirality : 0.038 0.141 1420 Planarity : 0.003 0.043 1447 Dihedral : 19.475 113.808 1727 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.58 % Allowed : 12.41 % 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: -0.14 (0.27), residues: 985 helix: 1.73 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 208 loop : -1.89 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1040 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 0.003 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9177) covalent geometry : angle 0.51443 / 0.29 (12645) hydrogen bonds : bond 0.04410 / 2.97 ( 411) hydrogen bonds : angle 4.00291 / 2.81 ( 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: 13 poor density : 34 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 901 HIS cc_start: 0.8489 (p-80) cc_final: 0.8255 (p-80) REVERT: B 974 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9184 (tt) REVERT: C 409 ASP cc_start: 0.8577 (t0) cc_final: 0.7784 (t0) REVERT: C 465 ARG cc_start: 0.8417 (mmt180) cc_final: 0.7812 (mmt180) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.0875 time to fit residues: 6.2273 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 : 0.315 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.064349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.044385 restraints weight = 30580.799| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.35 r_work: 0.2619 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9177 Z= 0.155 Angle : 0.525 6.104 12645 Z= 0.293 Chirality : 0.038 0.138 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.543 113.937 1727 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.70 % Allowed : 12.41 % Favored : 85.89 % 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: 1.74 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 208 loop : -1.90 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 426 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 0.00342 / 0.15 ( 9177) covalent geometry : angle 0.52487 / 0.29 (12645) hydrogen bonds : bond 0.04664 / 3.14 ( 411) hydrogen bonds : angle 4.01510 / 2.82 ( 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 901 HIS cc_start: 0.8489 (p-80) cc_final: 0.8284 (p-80) REVERT: B 974 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9178 (tt) REVERT: C 409 ASP cc_start: 0.8585 (t0) cc_final: 0.7790 (t0) REVERT: C 465 ARG cc_start: 0.8438 (mmt180) cc_final: 0.7830 (mmt180) outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.0834 time to fit residues: 6.1813 Evaluate side-chains 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 overall best weight: 0.9712 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.065230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.045383 restraints weight = 30239.769| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.31 r_work: 0.2646 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1657 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= 0.120 Angle : 0.497 6.169 12645 Z= 0.279 Chirality : 0.037 0.142 1420 Planarity : 0.003 0.044 1447 Dihedral : 19.544 113.319 1727 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.34 % Allowed : 13.14 % 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: -0.02 (0.27), residues: 985 helix: 1.86 (0.27), residues: 399 sheet: -0.47 (0.35), residues: 208 loop : -1.85 (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 0.006 0.001 PHE A 221 TRP 0.008 0.001 TRP B 128 HIS 0.002 0.000 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 9177) covalent geometry : angle 0.49716 / 0.28 (12645) hydrogen bonds : bond 0.03887 / 2.62 ( 411) hydrogen bonds : angle 3.85928 / 2.71 ( 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 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 901 HIS cc_start: 0.8490 (p-80) cc_final: 0.8289 (p-80) REVERT: B 974 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9178 (tt) REVERT: C 409 ASP cc_start: 0.8561 (t0) cc_final: 0.7766 (t0) REVERT: C 465 ARG cc_start: 0.8382 (mmt180) cc_final: 0.7761 (mmt180) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.0915 time to fit residues: 6.0982 Evaluate side-chains 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 85 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.063759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.044059 restraints weight = 30207.241| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.25 r_work: 0.2620 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9177 Z= 0.235 Angle : 0.593 10.756 12645 Z= 0.322 Chirality : 0.040 0.130 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.671 114.005 1727 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.34 % Allowed : 13.26 % 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: -0.23 (0.27), residues: 985 helix: 1.67 (0.27), residues: 399 sheet: -0.48 (0.35), residues: 203 loop : -1.99 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.014 0.002 TYR B 862 PHE 0.010 0.001 PHE B 187 TRP 0.008 0.001 TRP B 128 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 ( 9177) covalent geometry : angle 0.59340 / 0.32 (12645) hydrogen bonds : bond 0.05580 / 3.74 ( 411) hydrogen bonds : angle 4.16526 / 2.92 ( 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 43 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8540 (p-80) cc_final: 0.8311 (p-80) REVERT: B 974 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9181 (tt) REVERT: C 409 ASP cc_start: 0.8608 (t0) cc_final: 0.7804 (t0) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.0791 time to fit residues: 5.3715 Evaluate side-chains 41 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 14 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.065238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045148 restraints weight = 30573.914| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.40 r_work: 0.2642 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9177 Z= 0.110 Angle : 0.510 10.959 12645 Z= 0.282 Chirality : 0.037 0.146 1420 Planarity : 0.003 0.043 1447 Dihedral : 19.557 112.551 1727 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.22 % Allowed : 13.26 % 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: -0.04 (0.27), residues: 985 helix: 1.85 (0.27), residues: 399 sheet: -0.48 (0.35), residues: 208 loop : -1.87 (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 0.003 0.001 HIS A 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 9177) covalent geometry : angle 0.51029 / 0.28 (12645) hydrogen bonds : bond 0.03836 / 2.58 ( 411) hydrogen bonds : angle 3.84547 / 2.69 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.34 seconds wall clock time: 33 minutes 12.46 seconds (1992.46 seconds total)