Starting phenix.real_space_refine on Thu Feb 13 15:39:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_27482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_27482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_27482.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_27482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/02_2025/8dk3_27482.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.64, per 1000 atoms: 0.63 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: 2.29 Conformation dependent library (CDL) restraints added in 928.9 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: 3.02 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: 2.84 Time building geometry restraints manager: 2.65 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 1083 or resid 1201 thr \ ough 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.880 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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= 0.380 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.008 0.001 TRP A 128 HIS 0.005 0.001 HIS B1045 PHE 0.013 0.001 PHE B 187 TYR 0.012 0.001 TYR B 862 ARG 0.003 0.000 ARG B1059 *********************** 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 : 0.945 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: 0.2644 time to fit residues: 17.9615 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 : 1.044 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 93 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.065709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.045996 restraints weight = 29740.227| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.27 r_work: 0.2672 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1079 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= 0.155 Angle : 0.542 6.548 12645 Z= 0.297 Chirality : 0.038 0.159 1420 Planarity : 0.004 0.042 1447 Dihedral : 18.950 114.817 1751 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.97 % Allowed : 8.15 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 985 helix: 1.74 (0.27), residues: 402 sheet: -0.27 (0.36), residues: 205 loop : -1.72 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 901 PHE 0.007 0.001 PHE C 467 TYR 0.014 0.001 TYR B 862 ARG 0.007 0.000 ARG A 883 *********************** 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8500 (p-80) cc_final: 0.8267 (p-80) REVERT: C 409 ASP cc_start: 0.8460 (t0) cc_final: 0.7708 (t0) REVERT: C 495 ILE cc_start: 0.9027 (tp) cc_final: 0.8764 (pt) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.1877 time to fit residues: 13.3882 Evaluate side-chains 38 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 95 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.0270 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.066055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046229 restraints weight = 30531.527| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.32 r_work: 0.2678 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9177 Z= 0.142 Angle : 0.486 5.402 12645 Z= 0.271 Chirality : 0.037 0.144 1420 Planarity : 0.003 0.046 1447 Dihedral : 18.829 108.712 1748 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.22 % Allowed : 9.12 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 985 helix: 1.85 (0.27), residues: 403 sheet: -0.22 (0.35), residues: 208 loop : -1.69 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 128 HIS 0.003 0.000 HIS A 901 PHE 0.008 0.001 PHE C 467 TYR 0.014 0.001 TYR B 862 ARG 0.003 0.000 ARG A 883 *********************** 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: 10 poor density : 36 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8480 (p-80) cc_final: 0.8277 (p-80) REVERT: C 409 ASP cc_start: 0.8467 (t0) cc_final: 0.7652 (t0) REVERT: C 465 ARG cc_start: 0.8395 (mmt180) cc_final: 0.7807 (mmt180) REVERT: C 495 ILE cc_start: 0.8969 (tp) cc_final: 0.8716 (pt) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.2061 time to fit residues: 14.2783 Evaluate side-chains 41 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.063491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.043390 restraints weight = 30977.952| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.37 r_work: 0.2593 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 9177 Z= 0.407 Angle : 0.612 5.965 12645 Z= 0.331 Chirality : 0.041 0.145 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.008 108.809 1748 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.34 % Allowed : 10.71 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 985 helix: 1.63 (0.27), residues: 400 sheet: -0.35 (0.35), residues: 205 loop : -1.91 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.006 0.001 HIS B1045 PHE 0.013 0.002 PHE B 187 TYR 0.015 0.002 TYR B 862 ARG 0.003 0.000 ARG A 78 *********************** 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 48 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8537 (p-80) cc_final: 0.8315 (p-80) REVERT: C 409 ASP cc_start: 0.8548 (t0) cc_final: 0.7766 (t0) REVERT: C 465 ARG cc_start: 0.8458 (mmt180) cc_final: 0.7791 (mmt180) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.1988 time to fit residues: 14.5402 Evaluate side-chains 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.064480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.044424 restraints weight = 30651.771| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.36 r_work: 0.2616 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 9177 Z= 0.227 Angle : 0.532 8.536 12645 Z= 0.292 Chirality : 0.038 0.138 1420 Planarity : 0.004 0.044 1447 Dihedral : 18.959 103.927 1748 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.58 % Allowed : 11.07 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 985 helix: 1.71 (0.27), residues: 400 sheet: -0.37 (0.35), residues: 205 loop : -1.86 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 PHE 0.008 0.001 PHE A 221 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG C 426 *********************** 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 49 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8508 (p-80) cc_final: 0.8278 (p-80) REVERT: B 974 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9170 (tt) REVERT: C 409 ASP cc_start: 0.8588 (t0) cc_final: 0.7801 (t0) REVERT: C 465 ARG cc_start: 0.8444 (mmt180) cc_final: 0.7835 (mmt180) outliers start: 13 outliers final: 7 residues processed: 49 average time/residue: 0.2069 time to fit residues: 15.1845 Evaluate side-chains 43 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.063086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043283 restraints weight = 30232.713| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.26 r_work: 0.2589 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1415 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= 0.417 Angle : 0.627 8.887 12645 Z= 0.339 Chirality : 0.041 0.152 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.094 102.906 1748 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.58 % Allowed : 11.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 985 helix: 1.44 (0.27), residues: 400 sheet: -0.54 (0.35), residues: 205 loop : -2.01 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.007 0.001 HIS B1045 PHE 0.013 0.002 PHE B 187 TYR 0.014 0.002 TYR B 862 ARG 0.004 0.000 ARG B 969 *********************** 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 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8501 (p-80) cc_final: 0.8269 (p-80) REVERT: C 409 ASP cc_start: 0.8637 (t0) cc_final: 0.7843 (t0) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1828 time to fit residues: 12.4560 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 : 0.940 ------------------------------------------------------------------------------- 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 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 462 THR 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 91 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.064695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044658 restraints weight = 30646.724| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.37 r_work: 0.2622 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9177 Z= 0.175 Angle : 0.529 9.444 12645 Z= 0.289 Chirality : 0.037 0.142 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.015 98.597 1748 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.09 % Allowed : 12.04 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 985 helix: 1.72 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 208 loop : -1.88 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 PHE 0.008 0.001 PHE A 221 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG A1040 *********************** 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 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7800 (tt) REVERT: C 409 ASP cc_start: 0.8585 (t0) cc_final: 0.7797 (t0) outliers start: 9 outliers final: 8 residues processed: 41 average time/residue: 0.1872 time to fit residues: 12.1619 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 : 1.059 ------------------------------------------------------------------------------- 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 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 462 THR 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 11 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.064127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044324 restraints weight = 30392.229| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.29 r_work: 0.2628 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9177 Z= 0.263 Angle : 0.561 10.390 12645 Z= 0.302 Chirality : 0.038 0.140 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.079 99.840 1748 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.95 % Allowed : 11.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 985 helix: 1.68 (0.27), residues: 400 sheet: -0.55 (0.35), residues: 208 loop : -1.89 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.010 0.001 HIS A 901 PHE 0.008 0.001 PHE B 187 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 *********************** 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 49 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (tt) REVERT: C 409 ASP cc_start: 0.8600 (t0) cc_final: 0.7806 (t0) outliers start: 16 outliers final: 10 residues processed: 49 average time/residue: 0.1762 time to fit residues: 13.6307 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 : 0.951 ------------------------------------------------------------------------------- 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 41 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.063353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.043485 restraints weight = 30424.994| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.28 r_work: 0.2602 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9177 Z= 0.360 Angle : 0.613 10.766 12645 Z= 0.328 Chirality : 0.040 0.148 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.165 100.778 1748 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.58 % Allowed : 12.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 985 helix: 1.49 (0.27), residues: 399 sheet: -0.52 (0.35), residues: 203 loop : -1.99 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.006 0.001 HIS B1045 PHE 0.010 0.001 PHE B 187 TYR 0.014 0.002 TYR B 862 ARG 0.002 0.000 ARG A1026 *********************** 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 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 409 ASP cc_start: 0.8613 (t0) cc_final: 0.7863 (t0) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.1863 time to fit residues: 13.2291 Evaluate side-chains 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 153 LEU 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 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 55 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.064677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.044818 restraints weight = 29979.949| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.28 r_work: 0.2642 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9177 Z= 0.192 Angle : 0.544 11.166 12645 Z= 0.293 Chirality : 0.037 0.142 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.097 96.799 1748 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.97 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 985 helix: 1.74 (0.27), residues: 398 sheet: -0.54 (0.35), residues: 208 loop : -1.90 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 PHE 0.007 0.001 PHE A 221 TYR 0.015 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 ********************** 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 41 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7760 (tt) REVERT: C 409 ASP cc_start: 0.8573 (t0) cc_final: 0.7828 (t0) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1822 time to fit residues: 11.6439 Evaluate side-chains 41 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain B residue 145 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 71 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.0470 chunk 12 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.063480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.043678 restraints weight = 30176.394| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.25 r_work: 0.2606 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9177 Z= 0.360 Angle : 0.611 11.093 12645 Z= 0.327 Chirality : 0.040 0.139 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.184 99.945 1748 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.34 % Allowed : 12.90 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 985 helix: 1.57 (0.27), residues: 399 sheet: -0.53 (0.35), residues: 203 loop : -1.99 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.006 0.001 HIS B1045 PHE 0.011 0.001 PHE B 187 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3850.23 seconds wall clock time: 69 minutes 9.49 seconds (4149.49 seconds total)