Starting phenix.real_space_refine on Thu Mar 13 18:28:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk3_27482/03_2025/8dk3_27482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk3_27482/03_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_27482/03_2025/8dk3_27482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_2025/8dk3_27482.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_2025/8dk3_27482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk3_27482/03_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-5624/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: 5.65, 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: 2.35 Conformation dependent library (CDL) restraints added in 955.1 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: 2.94 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: 3.47 Time building geometry restraints manager: 2.76 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.340 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- 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 : 0.973 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: 0.2590 time to fit residues: 17.7202 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 : 0.737 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.045996 restraints weight = 29740.248| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.27 r_work: 0.2671 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- 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 : 0.957 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8496 (p-80) cc_final: 0.8263 (p-80) REVERT: C 409 ASP cc_start: 0.8468 (t0) cc_final: 0.7720 (t0) REVERT: C 495 ILE cc_start: 0.9022 (tp) cc_final: 0.8753 (pt) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.1838 time to fit residues: 13.2270 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 : 0.939 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 84 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.066000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.046080 restraints weight = 30468.309| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.32 r_work: 0.2678 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.002 0.023 9177 Z= 0.140 Angle : 0.486 5.488 12645 Z= 0.271 Chirality : 0.036 0.144 1420 Planarity : 0.003 0.046 1447 Dihedral : 18.827 108.627 1748 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.09 % Allowed : 9.25 % 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: -0.21 (0.35), residues: 208 loop : -1.69 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.003 0.000 HIS A 901 PHE 0.007 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 45 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8480 (p-80) cc_final: 0.8279 (p-80) REVERT: C 409 ASP cc_start: 0.8471 (t0) cc_final: 0.7659 (t0) REVERT: C 465 ARG cc_start: 0.8398 (mmt180) cc_final: 0.7809 (mmt180) REVERT: C 495 ILE cc_start: 0.8967 (tp) cc_final: 0.8716 (pt) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1991 time to fit residues: 13.8608 Evaluate side-chains 40 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.063607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.043493 restraints weight = 30920.687| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.38 r_work: 0.2591 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1232 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= 0.365 Angle : 0.597 5.900 12645 Z= 0.324 Chirality : 0.040 0.140 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.014 108.177 1748 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.46 % Allowed : 10.46 % Favored : 88.08 % 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 (0.27), residues: 985 helix: 1.66 (0.27), residues: 400 sheet: -0.34 (0.35), residues: 205 loop : -1.89 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS B1045 PHE 0.012 0.001 PHE B 187 TYR 0.014 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 49 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8532 (p-80) cc_final: 0.8309 (p-80) REVERT: C 409 ASP cc_start: 0.8597 (t0) cc_final: 0.7818 (t0) REVERT: C 465 ARG cc_start: 0.8451 (mmt180) cc_final: 0.7782 (mmt180) outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 0.1934 time to fit residues: 14.7186 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 : 0.942 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.064747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.044944 restraints weight = 29986.791| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.28 r_work: 0.2632 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9177 Z= 0.214 Angle : 0.526 7.160 12645 Z= 0.289 Chirality : 0.038 0.140 1420 Planarity : 0.003 0.044 1447 Dihedral : 18.953 103.503 1748 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.34 % Allowed : 11.07 % Favored : 87.59 % 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: -0.06 (0.27), residues: 985 helix: 1.76 (0.27), residues: 399 sheet: -0.43 (0.35), residues: 208 loop : -1.82 (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 0.001 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 47 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8495 (p-80) cc_final: 0.8265 (p-80) REVERT: B 974 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 409 ASP cc_start: 0.8583 (t0) cc_final: 0.7789 (t0) REVERT: C 465 ARG cc_start: 0.8457 (mmt180) cc_final: 0.7867 (mmt180) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.2320 time to fit residues: 16.7587 Evaluate side-chains 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 102 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.063001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043224 restraints weight = 30208.895| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.25 r_work: 0.2593 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 9177 Z= 0.432 Angle : 0.637 8.825 12645 Z= 0.344 Chirality : 0.042 0.161 1420 Planarity : 0.004 0.046 1447 Dihedral : 19.110 103.220 1748 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.70 % Allowed : 11.07 % Favored : 87.23 % 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: -0.39 (0.27), residues: 985 helix: 1.42 (0.27), residues: 400 sheet: -0.49 (0.35), residues: 203 loop : -2.00 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 128 HIS 0.007 0.001 HIS B1045 PHE 0.013 0.002 PHE B 187 TYR 0.014 0.002 TYR A 891 ARG 0.003 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 46 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8508 (p-80) cc_final: 0.8274 (p-80) REVERT: C 409 ASP cc_start: 0.8641 (t0) cc_final: 0.7843 (t0) outliers start: 14 outliers final: 12 residues processed: 44 average time/residue: 0.2097 time to fit residues: 14.8382 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 : 1.054 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.064862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044807 restraints weight = 30609.789| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.39 r_work: 0.2631 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9177 Z= 0.164 Angle : 0.531 9.679 12645 Z= 0.288 Chirality : 0.037 0.146 1420 Planarity : 0.003 0.045 1447 Dihedral : 19.006 97.989 1748 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: -0.13 (0.27), residues: 985 helix: 1.74 (0.27), residues: 399 sheet: -0.51 (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 0.007 0.001 PHE A 221 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 *********************** 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 43 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8583 (t0) cc_final: 0.7797 (t0) REVERT: C 465 ARG cc_start: 0.8385 (mmt180) cc_final: 0.7799 (mmt180) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.2045 time to fit residues: 13.6022 Evaluate side-chains 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.063625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.043734 restraints weight = 30653.939| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.31 r_work: 0.2607 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1510 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= 0.325 Angle : 0.588 10.130 12645 Z= 0.316 Chirality : 0.039 0.142 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.112 100.793 1748 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.58 % Allowed : 11.80 % Favored : 86.62 % 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: -0.25 (0.27), residues: 985 helix: 1.62 (0.27), residues: 399 sheet: -0.51 (0.35), residues: 205 loop : -1.95 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS A 901 PHE 0.010 0.001 PHE B 187 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG A 78 *********************** 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 : 0.937 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8613 (t0) cc_final: 0.7807 (t0) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.2167 time to fit residues: 16.3885 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 : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.064304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.044496 restraints weight = 30175.622| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.26 r_work: 0.2630 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9177 Z= 0.246 Angle : 0.557 10.824 12645 Z= 0.300 Chirality : 0.038 0.138 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.102 98.687 1748 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.34 % Allowed : 12.77 % 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: -0.20 (0.27), residues: 985 helix: 1.69 (0.27), residues: 398 sheet: -0.57 (0.35), residues: 208 loop : -1.91 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS B1045 PHE 0.007 0.001 PHE A 221 TYR 0.014 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8588 (t0) cc_final: 0.7845 (t0) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.2549 time to fit residues: 17.9221 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 : 1.064 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.064405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.044576 restraints weight = 29963.882| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.26 r_work: 0.2635 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9177 Z= 0.237 Angle : 0.555 11.170 12645 Z= 0.299 Chirality : 0.038 0.139 1420 Planarity : 0.004 0.044 1447 Dihedral : 19.123 98.433 1748 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.09 % Allowed : 13.02 % 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: -0.17 (0.27), residues: 985 helix: 1.73 (0.27), residues: 398 sheet: -0.55 (0.35), residues: 208 loop : -1.91 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 PHE 0.007 0.001 PHE A 221 TYR 0.014 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 42 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8579 (t0) cc_final: 0.7833 (t0) outliers start: 9 outliers final: 9 residues processed: 42 average time/residue: 0.2018 time to fit residues: 13.6572 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 : 3.136 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 = 0.063075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.043173 restraints weight = 30276.782| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.29 r_work: 0.2603 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9177 Z= 0.399 Angle : 0.636 11.006 12645 Z= 0.340 Chirality : 0.041 0.155 1420 Planarity : 0.004 0.045 1447 Dihedral : 19.207 100.571 1748 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.09 % Allowed : 13.02 % 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: -0.42 (0.27), residues: 985 helix: 1.46 (0.27), residues: 399 sheet: -0.59 (0.35), residues: 203 loop : -2.03 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS B1045 PHE 0.012 0.001 PHE B 187 TYR 0.014 0.002 TYR B 862 ARG 0.002 0.000 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.13 seconds wall clock time: 73 minutes 28.96 seconds (4408.96 seconds total)