Starting phenix.real_space_refine on Tue Mar 3 22:57:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk3_27482/03_2026/8dk3_27482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/03_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_27482/03_2026/8dk3_27482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_2026/8dk3_27482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_2026/8dk3_27482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_2026/8dk3_27482.map" } 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-5986/lib/python3.9/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: 2.23, per 1000 atoms: 0.25 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: 0.78 Conformation dependent library (CDL) restraints added in 328.1 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: 0.97 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: 1.76 Time building geometry restraints manager: 1.06 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=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 1.464 1.454 0.010 9.80e-03 1.04e+04 9.60e-01 bond pdb=" CB VAL A 197 " pdb=" CG1 VAL A 197 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.73e-01 bond pdb=" CB VAL B1068 " pdb=" CG2 VAL B1068 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.55e-01 bond pdb=" CB THR B1062 " pdb=" CG2 THR B1062 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.54e-01 bond pdb=" CA THR B 88 " pdb=" CB THR B 88 " ideal model delta sigma weight residual 1.531 1.501 0.029 3.28e-02 9.30e+02 8.05e-01 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 12079 1.26 - 2.52: 488 2.52 - 3.78: 64 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=" CA GLU C 475 " pdb=" C GLU C 475 " pdb=" N GLN C 476 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 angle pdb=" N GLY B1016 " pdb=" CA GLY B1016 " pdb=" C GLY B1016 " ideal model delta sigma weight residual 113.18 118.20 -5.02 2.37e+00 1.78e-01 4.49e+00 angle pdb=" N GLU C 475 " pdb=" CA GLU C 475 " pdb=" C GLU C 475 " ideal model delta sigma weight residual 108.31 111.46 -3.15 1.52e+00 4.33e-01 4.28e+00 angle pdb=" C ALA B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 122.28 120.54 1.74 8.80e-01 1.29e+00 3.93e+00 ... (remaining 12640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.79: 4886 22.79 - 45.58: 366 45.58 - 68.38: 135 68.38 - 91.17: 1 91.17 - 113.96: 1 Dihedral angle restraints: 5389 sinusoidal: 2542 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 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 744 0.026 - 0.053: 441 0.053 - 0.079: 143 0.079 - 0.105: 62 0.105 - 0.132: 30 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: 2.470 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 0.031 9177 Z= 0.248 Angle : 0.579 6.299 12645 Z= 0.320 Chirality : 0.040 0.132 1420 Planarity : 0.004 0.046 1447 Dihedral : 16.396 113.958 3555 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 covalent geometry : bond 0.00579 ( 9177) covalent geometry : angle 0.57950 (12645) hydrogen bonds : bond 0.20241 ( 411) hydrogen bonds : angle 6.21928 ( 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 : 0.282 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: 0.1060 time to fit residues: 7.2235 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3320 r_free = 0.3320 target = 0.064656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.044706 restraints weight = 30698.386| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.36 r_work: 0.2621 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0969 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= 0.154 Angle : 0.558 6.505 12645 Z= 0.306 Chirality : 0.039 0.148 1420 Planarity : 0.004 0.042 1447 Dihedral : 18.989 113.722 1751 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.97 % Allowed : 8.88 % Favored : 90.15 % 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: 1.68 (0.27), residues: 401 sheet: -0.35 (0.36), residues: 205 loop : -1.75 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 883 TYR 0.014 0.001 TYR B 862 PHE 0.007 0.001 PHE B1048 TRP 0.007 0.001 TRP A 128 HIS 0.004 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9177) covalent geometry : angle 0.55777 (12645) hydrogen bonds : bond 0.05234 ( 411) hydrogen bonds : angle 4.49748 ( 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: 8 poor density : 37 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8505 (p-80) cc_final: 0.8269 (p-80) REVERT: C 409 ASP cc_start: 0.8503 (t0) cc_final: 0.7766 (t0) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.0710 time to fit residues: 4.9747 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 : 0.299 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 944 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.042488 restraints weight = 31348.355| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.36 r_work: 0.2559 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 9177 Z= 0.297 Angle : 0.659 7.565 12645 Z= 0.356 Chirality : 0.043 0.168 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.065 108.168 1749 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.95 % Allowed : 9.73 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.27), residues: 985 helix: 1.37 (0.27), residues: 399 sheet: -0.51 (0.35), residues: 203 loop : -1.98 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 883 TYR 0.015 0.002 TYR B 862 PHE 0.014 0.002 PHE B 187 TRP 0.010 0.002 TRP A 128 HIS 0.007 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 9177) covalent geometry : angle 0.65854 (12645) hydrogen bonds : bond 0.06966 ( 411) hydrogen bonds : angle 4.60846 ( 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 50 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8497 (p-80) cc_final: 0.8257 (p-80) REVERT: C 409 ASP cc_start: 0.8556 (t0) cc_final: 0.7811 (t0) outliers start: 16 outliers final: 9 residues processed: 48 average time/residue: 0.0653 time to fit residues: 4.9548 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 : 0.308 ------------------------------------------------------------------------------- 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 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 495 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.044842 restraints weight = 31303.276| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.41 r_work: 0.2638 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1414 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= 0.121 Angle : 0.520 7.219 12645 Z= 0.287 Chirality : 0.037 0.145 1420 Planarity : 0.004 0.046 1447 Dihedral : 18.911 102.162 1749 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 1.82 % Allowed : 10.46 % Favored : 87.71 % 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: 1.67 (0.27), residues: 400 sheet: -0.55 (0.35), residues: 208 loop : -1.87 (0.29), residues: 377 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 A 221 TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 901 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9177) covalent geometry : angle 0.52033 (12645) hydrogen bonds : bond 0.04094 ( 411) hydrogen bonds : angle 4.06809 ( 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 51 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8501 (p-80) cc_final: 0.8257 (p-80) REVERT: B 223 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 974 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9178 (tt) REVERT: C 409 ASP cc_start: 0.8539 (t0) cc_final: 0.7749 (t0) REVERT: C 465 ARG cc_start: 0.8433 (mmt180) cc_final: 0.7850 (mmt180) outliers start: 15 outliers final: 9 residues processed: 49 average time/residue: 0.0844 time to fit residues: 6.1678 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 : 0.298 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 223 GLU 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 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043166 restraints weight = 30552.356| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.27 r_work: 0.2586 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.006 0.034 9177 Z= 0.270 Angle : 0.622 6.003 12645 Z= 0.336 Chirality : 0.041 0.145 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.114 104.185 1749 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.07 % Allowed : 11.80 % 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: -0.43 (0.27), residues: 985 helix: 1.46 (0.27), residues: 399 sheet: -0.57 (0.35), residues: 203 loop : -2.05 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.015 0.002 TYR B 862 PHE 0.012 0.002 PHE B 187 TRP 0.010 0.002 TRP B 128 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 9177) covalent geometry : angle 0.62195 (12645) hydrogen bonds : bond 0.06298 ( 411) hydrogen bonds : angle 4.38017 ( 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: 17 poor density : 33 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8492 (p-80) cc_final: 0.8257 (p-80) REVERT: B 223 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 409 ASP cc_start: 0.8639 (t0) cc_final: 0.7858 (t0) outliers start: 17 outliers final: 11 residues processed: 47 average time/residue: 0.0731 time to fit residues: 5.3845 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 : 0.302 ------------------------------------------------------------------------------- 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 223 GLU 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 495 ILE 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: 3.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.044429 restraints weight = 30149.049| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.25 r_work: 0.2626 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 9177 Z= 0.155 Angle : 0.540 6.085 12645 Z= 0.296 Chirality : 0.038 0.139 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.056 99.306 1749 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.82 % Allowed : 12.17 % 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: -0.27 (0.27), residues: 985 helix: 1.60 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 203 loop : -1.95 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 426 TYR 0.015 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 covalent geometry : bond 0.00351 ( 9177) covalent geometry : angle 0.53952 (12645) hydrogen bonds : bond 0.04713 ( 411) hydrogen bonds : angle 4.10567 ( 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 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 409 ASP cc_start: 0.8604 (t0) cc_final: 0.7810 (t0) outliers start: 15 outliers final: 11 residues processed: 45 average time/residue: 0.0741 time to fit residues: 5.2255 Evaluate side-chains 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 904 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 Chi-restraints excluded: chain C residue 495 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044229 restraints weight = 30343.136| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.29 r_work: 0.2621 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9177 Z= 0.162 Angle : 0.546 9.498 12645 Z= 0.297 Chirality : 0.038 0.139 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.100 99.409 1749 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.31 % Allowed : 12.04 % 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: -0.24 (0.27), residues: 985 helix: 1.65 (0.27), residues: 399 sheet: -0.59 (0.35), residues: 206 loop : -1.92 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 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 0.008 0.001 HIS A 901 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9177) covalent geometry : angle 0.54596 (12645) hydrogen bonds : bond 0.04769 ( 411) hydrogen bonds : angle 4.05714 ( 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 51 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: B 974 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9203 (tt) REVERT: C 409 ASP cc_start: 0.8607 (t0) cc_final: 0.7809 (t0) outliers start: 19 outliers final: 12 residues processed: 49 average time/residue: 0.0701 time to fit residues: 5.4011 Evaluate side-chains 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 904 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 Chi-restraints excluded: chain C residue 495 ILE 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: 0.9990 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.045704 restraints weight = 29944.225| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.26 r_work: 0.2664 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1712 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= 0.116 Angle : 0.508 5.923 12645 Z= 0.279 Chirality : 0.037 0.145 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.074 96.259 1749 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.58 % Allowed : 13.14 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.27), residues: 985 helix: 1.80 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 208 loop : -1.84 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 969 TYR 0.014 0.001 TYR B 862 PHE 0.006 0.001 PHE B 886 TRP 0.007 0.001 TRP B 128 HIS 0.004 0.000 HIS A 901 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9177) covalent geometry : angle 0.50827 (12645) hydrogen bonds : bond 0.03684 ( 411) hydrogen bonds : angle 3.83037 ( 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: B 974 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9193 (tt) REVERT: C 409 ASP cc_start: 0.8577 (t0) cc_final: 0.7774 (t0) REVERT: C 465 ARG cc_start: 0.8359 (mmt180) cc_final: 0.7766 (mmt180) outliers start: 13 outliers final: 10 residues processed: 45 average time/residue: 0.0874 time to fit residues: 5.8832 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 : 0.323 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 904 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.043819 restraints weight = 30305.190| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.28 r_work: 0.2609 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1599 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= 0.221 Angle : 0.579 6.677 12645 Z= 0.314 Chirality : 0.040 0.134 1420 Planarity : 0.004 0.047 1447 Dihedral : 19.163 99.539 1749 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.70 % Allowed : 12.77 % 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: -0.24 (0.27), residues: 985 helix: 1.68 (0.27), residues: 399 sheet: -0.66 (0.35), residues: 208 loop : -1.92 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.014 0.001 TYR B 862 PHE 0.010 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 covalent geometry : bond 0.00518 ( 9177) covalent geometry : angle 0.57939 (12645) hydrogen bonds : bond 0.05423 ( 411) hydrogen bonds : angle 4.10945 ( 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 409 ASP cc_start: 0.8614 (t0) cc_final: 0.7807 (t0) outliers start: 14 outliers final: 10 residues processed: 44 average time/residue: 0.0861 time to fit residues: 5.6866 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 : 0.311 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU 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 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 102 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.064531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.044696 restraints weight = 30080.528| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.26 r_work: 0.2637 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1656 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= 0.150 Angle : 0.536 6.728 12645 Z= 0.293 Chirality : 0.038 0.140 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.125 97.428 1749 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.20 (0.27), residues: 985 helix: 1.71 (0.27), residues: 399 sheet: -0.66 (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 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 0.003 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9177) covalent geometry : angle 0.53583 (12645) hydrogen bonds : bond 0.04583 ( 411) hydrogen bonds : angle 3.97390 ( 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 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: C 409 ASP cc_start: 0.8601 (t0) cc_final: 0.7791 (t0) outliers start: 12 outliers final: 10 residues processed: 43 average time/residue: 0.0714 time to fit residues: 4.7497 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 : 0.296 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 1001 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: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 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: 3.9990 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.043316 restraints weight = 30045.664| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.25 r_work: 0.2591 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 9177 Z= 0.255 Angle : 0.636 11.248 12645 Z= 0.338 Chirality : 0.041 0.155 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.197 99.684 1749 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.70 % Allowed : 13.02 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.45 (0.27), residues: 985 helix: 1.47 (0.27), residues: 399 sheet: -0.69 (0.35), residues: 203 loop : -2.03 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.014 0.002 TYR B 862 PHE 0.011 0.001 PHE B 187 TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9177) covalent geometry : angle 0.63567 (12645) hydrogen bonds : bond 0.06125 ( 411) hydrogen bonds : angle 4.29386 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.63 seconds wall clock time: 30 minutes 41.14 seconds (1841.14 seconds total)