Starting phenix.real_space_refine on Wed Sep 17 12:48:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivd_60925/09_2025/9ivd_60925.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 52 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 C 5544 2.51 5 N 1496 2.21 5 O 1544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8628 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 89 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2824 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 5715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5715 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 26, 'TRANS': 758} Chain breaks: 6 Unresolved non-hydrogen bonds: 478 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 48, 'ASP:plan': 23, 'ARG:plan': 9, 'GLN:plan1': 8, 'ASN:plan1': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 365 Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8628 At special positions: 0 Unit cell: (92.65, 111.35, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 1 15.00 O 1544 8.00 N 1496 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 346.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 27 sheets defined 5.9% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 8 through 18 removed outlier: 3.668A pdb=" N ARG B 18 " --> pdb=" O TRP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 891 through 895 removed outlier: 4.161A pdb=" N CYS B 895 " --> pdb=" O ASP B 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.668A pdb=" N LEU A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1131 through 1137 Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 46 removed outlier: 3.700A pdb=" N VAL B1034 " --> pdb=" O TYR B1026 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B1026 " --> pdb=" O VAL B1034 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 61 removed outlier: 4.714A pdb=" N LEU B 58 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 60 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 68 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS B 72 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 77 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER B 90 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 79 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.587A pdb=" N ALA B 198 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 197 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR B 859 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 903 through 906 removed outlier: 3.601A pdb=" N ALA B 922 " --> pdb=" O ALA B 906 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 949 removed outlier: 3.902A pdb=" N SER B 946 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 975 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 980 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 992 " --> pdb=" O ARG B 980 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 944 through 949 removed outlier: 3.902A pdb=" N SER B 946 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 975 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 997 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.262A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A1030 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.785A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 61 through 67 removed outlier: 7.033A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.975A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.543A pdb=" N ASP A 99 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.660A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 139 through 142 removed outlier: 3.690A pdb=" N VAL A 142 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 155 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.392A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 201 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.392A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 190 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.607A pdb=" N HIS A 240 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 246 " --> pdb=" O TYR A 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 258 through 263 removed outlier: 4.555A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 274 " --> pdb=" O CYS A 260 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 301 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.910A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.874A pdb=" N LEU A 387 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 720 through 726 removed outlier: 6.678A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.476A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 815 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 819 " --> pdb=" O TYR A 828 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.476A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 815 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 819 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 852 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 870 through 873 removed outlier: 4.702A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 900 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 921 through 922 removed outlier: 3.829A pdb=" N LEU A 922 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 933 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.929A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 965 " --> pdb=" O CYS A 977 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 975 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2802 1.34 - 1.46: 1851 1.46 - 1.58: 4084 1.58 - 1.69: 4 1.69 - 1.81: 65 Bond restraints: 8806 Sorted by residual: bond pdb=" OG1 TPO E 286 " pdb=" P TPO E 286 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CG PRO B 63 " pdb=" CD PRO B 63 " ideal model delta sigma weight residual 1.503 1.319 0.184 3.40e-02 8.65e+02 2.92e+01 bond pdb=" N PRO B 63 " pdb=" CD PRO B 63 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" O2P TPO E 286 " pdb=" P TPO E 286 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O3P TPO E 286 " pdb=" P TPO E 286 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 11928 3.41 - 6.81: 60 6.81 - 10.22: 6 10.22 - 13.62: 3 13.62 - 17.03: 1 Bond angle restraints: 11998 Sorted by residual: angle pdb=" CA PRO B 63 " pdb=" N PRO B 63 " pdb=" CD PRO B 63 " ideal model delta sigma weight residual 112.00 94.97 17.03 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO B 63 " pdb=" CD PRO B 63 " pdb=" CG PRO B 63 " ideal model delta sigma weight residual 103.20 93.67 9.53 1.50e+00 4.44e-01 4.04e+01 angle pdb=" C ALA A 841 " pdb=" CA ALA A 841 " pdb=" CB ALA A 841 " ideal model delta sigma weight residual 115.79 109.24 6.55 1.19e+00 7.06e-01 3.03e+01 angle pdb=" N PRO B 63 " pdb=" CA PRO B 63 " pdb=" CB PRO B 63 " ideal model delta sigma weight residual 103.52 98.80 4.72 1.06e+00 8.90e-01 1.99e+01 angle pdb=" CB TPO E 286 " pdb=" OG1 TPO E 286 " pdb=" P TPO E 286 " ideal model delta sigma weight residual 119.31 106.82 12.49 3.00e+00 1.11e-01 1.73e+01 ... (remaining 11993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4487 17.87 - 35.74: 530 35.74 - 53.61: 140 53.61 - 71.48: 20 71.48 - 89.35: 8 Dihedral angle restraints: 5185 sinusoidal: 1840 harmonic: 3345 Sorted by residual: dihedral pdb=" CA ALA B 157 " pdb=" C ALA B 157 " pdb=" N ASN B 158 " pdb=" CA ASN B 158 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ARG B 65 " pdb=" C ARG B 65 " pdb=" N THR B 66 " pdb=" CA THR B 66 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER A1075 " pdb=" C SER A1075 " pdb=" N PHE A1076 " pdb=" CA PHE A1076 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1263 0.077 - 0.155: 159 0.155 - 0.232: 1 0.232 - 0.310: 0 0.310 - 0.387: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA PRO B 63 " pdb=" N PRO B 63 " pdb=" C PRO B 63 " pdb=" CB PRO B 63 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA MET B 991 " pdb=" N MET B 991 " pdb=" C MET B 991 " pdb=" CB MET B 991 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA LEU A 926 " pdb=" N LEU A 926 " pdb=" C LEU A 926 " pdb=" CB LEU A 926 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 1421 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 62 " 0.112 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO B 63 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 184 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 185 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 104 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO B 105 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 105 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 105 " -0.025 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 218 2.68 - 3.24: 7582 3.24 - 3.79: 11857 3.79 - 4.35: 15007 4.35 - 4.90: 26151 Nonbonded interactions: 60815 Sorted by model distance: nonbonded pdb=" OG SER B 178 " pdb=" OE2 GLU B 181 " model vdw 2.128 3.040 nonbonded pdb=" O SER A 886 " pdb=" OG SER A 886 " model vdw 2.226 3.040 nonbonded pdb=" O TYR A 812 " pdb=" OG1 THR A 833 " model vdw 2.234 3.040 nonbonded pdb=" O SER B 52 " pdb=" OG SER B 52 " model vdw 2.237 3.040 nonbonded pdb=" O GLY A1010 " pdb=" OG SER A1027 " model vdw 2.251 3.040 ... (remaining 60810 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.004 0.184 8807 Z= 0.180 Angle : 0.719 17.026 12000 Z= 0.399 Chirality : 0.046 0.387 1424 Planarity : 0.005 0.153 1519 Dihedral : 16.740 89.349 3020 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.13 % Favored : 88.43 % Rotamer: Outliers : 0.23 % Allowed : 29.98 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.23), residues: 1132 helix: -1.72 (0.60), residues: 66 sheet: -1.45 (0.28), residues: 379 loop : -3.34 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1015 TYR 0.009 0.001 TYR A 906 PHE 0.012 0.001 PHE A 829 TRP 0.009 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8806) covalent geometry : angle 0.71878 (11998) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.34412 ( 2) hydrogen bonds : bond 0.29891 ( 189) hydrogen bonds : angle 9.70147 ( 564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.250 Fit side-chains REVERT: A 835 MET cc_start: 0.8431 (mtp) cc_final: 0.8221 (mtm) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.0929 time to fit residues: 7.7738 Evaluate side-chains 58 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 977 GLN A 727 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.057520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.046755 restraints weight = 35125.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048450 restraints weight = 16462.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.049660 restraints weight = 10227.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.050521 restraints weight = 7391.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.051081 restraints weight = 5820.556| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8807 Z= 0.114 Angle : 0.616 14.605 12000 Z= 0.319 Chirality : 0.045 0.152 1424 Planarity : 0.004 0.058 1519 Dihedral : 4.736 33.603 1236 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.31 % Favored : 88.25 % Rotamer: Outliers : 3.36 % Allowed : 27.89 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.23), residues: 1132 helix: -0.94 (0.65), residues: 63 sheet: -1.31 (0.27), residues: 405 loop : -3.34 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1015 TYR 0.012 0.001 TYR A 906 PHE 0.009 0.001 PHE A 829 TRP 0.008 0.001 TRP B 42 HIS 0.005 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8806) covalent geometry : angle 0.61505 (11998) SS BOND : bond 0.00269 ( 1) SS BOND : angle 2.16975 ( 2) hydrogen bonds : bond 0.03660 ( 189) hydrogen bonds : angle 6.20559 ( 564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.363 Fit side-chains REVERT: E 289 ASP cc_start: 0.8163 (t0) cc_final: 0.7870 (t0) REVERT: B 176 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8419 (p) outliers start: 29 outliers final: 9 residues processed: 83 average time/residue: 0.0827 time to fit residues: 10.2309 Evaluate side-chains 62 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 1036 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.053673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.042822 restraints weight = 35799.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.044366 restraints weight = 17331.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.045506 restraints weight = 11049.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.046195 restraints weight = 8094.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.046777 restraints weight = 6602.656| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8807 Z= 0.259 Angle : 0.683 12.947 12000 Z= 0.360 Chirality : 0.047 0.174 1424 Planarity : 0.004 0.058 1519 Dihedral : 5.196 36.341 1234 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.22 % Favored : 85.34 % Rotamer: Outliers : 4.28 % Allowed : 27.66 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.23), residues: 1132 helix: -0.96 (0.62), residues: 69 sheet: -1.34 (0.26), residues: 433 loop : -3.42 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 722 TYR 0.014 0.002 TYR B1026 PHE 0.014 0.001 PHE A 829 TRP 0.013 0.001 TRP B 42 HIS 0.007 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 8806) covalent geometry : angle 0.68291 (11998) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.65362 ( 2) hydrogen bonds : bond 0.04048 ( 189) hydrogen bonds : angle 5.75075 ( 564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 53 time to evaluate : 0.340 Fit side-chains REVERT: E 289 ASP cc_start: 0.8480 (t0) cc_final: 0.8144 (t0) REVERT: B 150 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: B 176 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 1041 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7323 (tt) REVERT: A 350 MET cc_start: 0.9610 (ptt) cc_final: 0.9278 (ptp) REVERT: A 870 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8928 (m) REVERT: A 1036 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (ptm) outliers start: 37 outliers final: 22 residues processed: 85 average time/residue: 0.0792 time to fit residues: 10.2487 Evaluate side-chains 78 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1028 THR Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 109 optimal weight: 0.0000 chunk 91 optimal weight: 0.0670 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.045152 restraints weight = 35733.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.046824 restraints weight = 16876.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.048020 restraints weight = 10533.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.048870 restraints weight = 7614.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.049507 restraints weight = 6028.839| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8807 Z= 0.096 Angle : 0.585 13.923 12000 Z= 0.300 Chirality : 0.045 0.153 1424 Planarity : 0.004 0.057 1519 Dihedral : 4.897 37.133 1234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.78 % Favored : 88.78 % Rotamer: Outliers : 3.70 % Allowed : 28.12 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.24), residues: 1132 helix: -0.63 (0.64), residues: 69 sheet: -1.22 (0.26), residues: 415 loop : -3.20 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.009 0.001 TYR B1026 PHE 0.009 0.001 PHE B 995 TRP 0.008 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8806) covalent geometry : angle 0.58486 (11998) SS BOND : bond 0.00155 ( 1) SS BOND : angle 1.57764 ( 2) hydrogen bonds : bond 0.02695 ( 189) hydrogen bonds : angle 5.15038 ( 564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.364 Fit side-chains REVERT: E 289 ASP cc_start: 0.8544 (t0) cc_final: 0.8146 (t0) REVERT: B 176 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 957 MET cc_start: 0.9162 (ttp) cc_final: 0.8698 (ttm) REVERT: A 350 MET cc_start: 0.9560 (ptt) cc_final: 0.9210 (ptp) REVERT: A 1036 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8481 (ptm) outliers start: 32 outliers final: 17 residues processed: 82 average time/residue: 0.0923 time to fit residues: 10.9544 Evaluate side-chains 71 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 885 GLN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.054147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.042903 restraints weight = 36722.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.044534 restraints weight = 16420.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.045715 restraints weight = 10140.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.046534 restraints weight = 7294.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.047093 restraints weight = 5832.312| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8807 Z= 0.249 Angle : 0.655 13.147 12000 Z= 0.342 Chirality : 0.046 0.165 1424 Planarity : 0.004 0.058 1519 Dihedral : 5.041 36.345 1234 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.31 % Favored : 85.25 % Rotamer: Outliers : 4.40 % Allowed : 28.24 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.23), residues: 1132 helix: -0.77 (0.63), residues: 74 sheet: -1.18 (0.26), residues: 429 loop : -3.36 (0.21), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 722 TYR 0.011 0.001 TYR B1026 PHE 0.009 0.001 PHE B 61 TRP 0.011 0.001 TRP B1016 HIS 0.006 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 8806) covalent geometry : angle 0.65474 (11998) SS BOND : bond 0.00067 ( 1) SS BOND : angle 1.28131 ( 2) hydrogen bonds : bond 0.03470 ( 189) hydrogen bonds : angle 5.28700 ( 564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.331 Fit side-chains REVERT: E 289 ASP cc_start: 0.8492 (t0) cc_final: 0.8124 (t0) REVERT: B 150 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: B 176 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 896 ASP cc_start: 0.9105 (t0) cc_final: 0.8753 (t0) REVERT: B 1041 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 218 MET cc_start: 0.8801 (mtp) cc_final: 0.8584 (ttt) REVERT: A 350 MET cc_start: 0.9534 (ptt) cc_final: 0.9169 (ptp) REVERT: A 870 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8792 (m) outliers start: 38 outliers final: 25 residues processed: 83 average time/residue: 0.0786 time to fit residues: 9.8514 Evaluate side-chains 78 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.053293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.042068 restraints weight = 36790.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.043638 restraints weight = 16785.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.044777 restraints weight = 10484.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.045611 restraints weight = 7646.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.046197 restraints weight = 6094.831| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8807 Z= 0.269 Angle : 0.682 12.622 12000 Z= 0.356 Chirality : 0.047 0.182 1424 Planarity : 0.004 0.055 1519 Dihedral : 5.346 40.022 1234 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.13 % Favored : 85.42 % Rotamer: Outliers : 5.09 % Allowed : 28.12 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.23), residues: 1132 helix: -0.64 (0.65), residues: 69 sheet: -1.21 (0.26), residues: 428 loop : -3.41 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.014 0.001 TYR B1026 PHE 0.010 0.001 PHE B 995 TRP 0.011 0.001 TRP B1016 HIS 0.007 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8806) covalent geometry : angle 0.68138 (11998) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.29652 ( 2) hydrogen bonds : bond 0.03525 ( 189) hydrogen bonds : angle 5.36499 ( 564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 50 time to evaluate : 0.384 Fit side-chains REVERT: E 289 ASP cc_start: 0.8581 (t0) cc_final: 0.8377 (t0) REVERT: B 41 LYS cc_start: 0.8962 (ttpp) cc_final: 0.8718 (ttpp) REVERT: B 86 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8160 (pttm) REVERT: B 176 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 861 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6520 (mtm-85) REVERT: B 896 ASP cc_start: 0.9126 (t0) cc_final: 0.8881 (t70) REVERT: B 1041 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7467 (tt) REVERT: A 350 MET cc_start: 0.9531 (ptt) cc_final: 0.9172 (ptp) REVERT: A 870 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8841 (m) outliers start: 44 outliers final: 33 residues processed: 88 average time/residue: 0.0769 time to fit residues: 10.2762 Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 861 ARG Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.054410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.043256 restraints weight = 36686.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.044908 restraints weight = 16462.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.046094 restraints weight = 10148.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.046944 restraints weight = 7291.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.047552 restraints weight = 5758.039| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8807 Z= 0.146 Angle : 0.609 12.652 12000 Z= 0.314 Chirality : 0.045 0.162 1424 Planarity : 0.004 0.057 1519 Dihedral : 5.114 43.157 1234 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.63 % Favored : 86.93 % Rotamer: Outliers : 4.28 % Allowed : 29.17 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.24), residues: 1132 helix: -0.33 (0.67), residues: 69 sheet: -1.15 (0.25), residues: 432 loop : -3.30 (0.21), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.011 0.001 TYR B1026 PHE 0.010 0.001 PHE B 61 TRP 0.010 0.001 TRP B1016 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8806) covalent geometry : angle 0.60836 (11998) SS BOND : bond 0.00126 ( 1) SS BOND : angle 1.36996 ( 2) hydrogen bonds : bond 0.02861 ( 189) hydrogen bonds : angle 5.04288 ( 564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 53 time to evaluate : 0.228 Fit side-chains REVERT: E 289 ASP cc_start: 0.8583 (t0) cc_final: 0.8029 (t0) REVERT: B 41 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8738 (ttpp) REVERT: B 150 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8696 (tt0) REVERT: B 176 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 896 ASP cc_start: 0.9071 (t0) cc_final: 0.8842 (t70) REVERT: B 946 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 952 MET cc_start: 0.9505 (mmm) cc_final: 0.9304 (mmm) REVERT: B 1041 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7485 (tt) REVERT: A 870 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8750 (m) outliers start: 37 outliers final: 25 residues processed: 87 average time/residue: 0.0853 time to fit residues: 10.8524 Evaluate side-chains 79 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 946 SER Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.044119 restraints weight = 36046.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.045816 restraints weight = 16331.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.047032 restraints weight = 10022.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.047876 restraints weight = 7140.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.048526 restraints weight = 5646.716| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8807 Z= 0.109 Angle : 0.598 12.668 12000 Z= 0.303 Chirality : 0.045 0.179 1424 Planarity : 0.004 0.054 1519 Dihedral : 4.938 44.162 1234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.75 % Favored : 87.81 % Rotamer: Outliers : 3.94 % Allowed : 29.40 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.24), residues: 1132 helix: -0.48 (0.64), residues: 75 sheet: -1.06 (0.26), residues: 424 loop : -3.14 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.009 0.001 TYR B1026 PHE 0.010 0.001 PHE B 61 TRP 0.010 0.001 TRP B1016 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8806) covalent geometry : angle 0.59799 (11998) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.47417 ( 2) hydrogen bonds : bond 0.02538 ( 189) hydrogen bonds : angle 4.78890 ( 564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.281 Fit side-chains REVERT: E 289 ASP cc_start: 0.8633 (t0) cc_final: 0.8403 (t0) REVERT: B 41 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8742 (ttpp) REVERT: B 150 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: B 176 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 896 ASP cc_start: 0.9048 (t0) cc_final: 0.8790 (t0) REVERT: B 946 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 960 LEU cc_start: 0.9371 (mp) cc_final: 0.9079 (mm) REVERT: B 1041 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 870 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8660 (m) outliers start: 34 outliers final: 25 residues processed: 84 average time/residue: 0.0727 time to fit residues: 9.4352 Evaluate side-chains 81 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 946 SER Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.042300 restraints weight = 36543.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.043927 restraints weight = 16733.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.045086 restraints weight = 10325.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.045819 restraints weight = 7482.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.046460 restraints weight = 6013.043| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8807 Z= 0.246 Angle : 0.673 11.802 12000 Z= 0.346 Chirality : 0.046 0.167 1424 Planarity : 0.004 0.057 1519 Dihedral : 5.155 43.766 1234 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.93 % Favored : 84.63 % Rotamer: Outliers : 4.17 % Allowed : 29.40 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.24), residues: 1132 helix: 0.04 (0.67), residues: 68 sheet: -1.05 (0.26), residues: 434 loop : -3.33 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.013 0.001 TYR B1026 PHE 0.010 0.001 PHE B 61 TRP 0.010 0.001 TRP B1016 HIS 0.007 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 8806) covalent geometry : angle 0.67329 (11998) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.11297 ( 2) hydrogen bonds : bond 0.03256 ( 189) hydrogen bonds : angle 5.06534 ( 564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.342 Fit side-chains REVERT: E 289 ASP cc_start: 0.8652 (t0) cc_final: 0.8098 (t0) REVERT: B 41 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8733 (ttpp) REVERT: B 150 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: B 176 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8361 (p) REVERT: B 861 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6498 (mtm-85) REVERT: B 896 ASP cc_start: 0.9101 (t0) cc_final: 0.8793 (t0) REVERT: B 934 MET cc_start: 0.8886 (tpp) cc_final: 0.8592 (tpp) REVERT: B 946 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8733 (p) REVERT: B 960 LEU cc_start: 0.9406 (mp) cc_final: 0.9103 (mm) REVERT: B 1041 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7522 (tt) REVERT: A 870 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8817 (m) outliers start: 36 outliers final: 28 residues processed: 81 average time/residue: 0.0822 time to fit residues: 9.9703 Evaluate side-chains 83 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 49 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 861 ARG Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 946 SER Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.043421 restraints weight = 36205.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.045060 restraints weight = 16099.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.046110 restraints weight = 9986.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.046996 restraints weight = 7399.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.047488 restraints weight = 5829.210| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8807 Z= 0.139 Angle : 0.625 12.039 12000 Z= 0.318 Chirality : 0.046 0.192 1424 Planarity : 0.004 0.053 1519 Dihedral : 5.082 45.534 1234 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.75 % Favored : 87.90 % Rotamer: Outliers : 4.17 % Allowed : 29.05 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.24), residues: 1132 helix: 0.16 (0.68), residues: 68 sheet: -1.03 (0.26), residues: 430 loop : -3.26 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 847 TYR 0.010 0.001 TYR B1026 PHE 0.010 0.001 PHE B 61 TRP 0.010 0.001 TRP B1016 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8806) covalent geometry : angle 0.62483 (11998) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.22451 ( 2) hydrogen bonds : bond 0.02734 ( 189) hydrogen bonds : angle 4.86224 ( 564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 51 time to evaluate : 0.375 Fit side-chains REVERT: E 289 ASP cc_start: 0.8625 (t0) cc_final: 0.8397 (t0) REVERT: B 150 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: B 176 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 861 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6437 (mtm-85) REVERT: B 896 ASP cc_start: 0.9100 (t0) cc_final: 0.8774 (t0) REVERT: B 934 MET cc_start: 0.8999 (tpp) cc_final: 0.8706 (tpp) REVERT: B 946 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8756 (p) REVERT: B 960 LEU cc_start: 0.9379 (mp) cc_final: 0.9081 (mm) REVERT: B 1041 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7521 (tt) REVERT: A 870 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8811 (m) outliers start: 36 outliers final: 27 residues processed: 82 average time/residue: 0.0828 time to fit residues: 10.2395 Evaluate side-chains 84 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 100 CYS Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 861 ARG Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 895 CYS Chi-restraints excluded: chain B residue 908 ILE Chi-restraints excluded: chain B residue 946 SER Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.044749 restraints weight = 35608.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.046503 restraints weight = 16053.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.047728 restraints weight = 9774.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.048478 restraints weight = 6984.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.049127 restraints weight = 5585.091| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8807 Z= 0.101 Angle : 0.613 14.967 12000 Z= 0.305 Chirality : 0.045 0.201 1424 Planarity : 0.004 0.056 1519 Dihedral : 4.821 46.170 1234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.75 % Favored : 87.90 % Rotamer: Outliers : 3.24 % Allowed : 29.98 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.24), residues: 1132 helix: -0.11 (0.66), residues: 75 sheet: -0.82 (0.27), residues: 405 loop : -3.10 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 739 TYR 0.008 0.001 TYR A 182 PHE 0.010 0.001 PHE B 61 TRP 0.009 0.001 TRP B1016 HIS 0.003 0.001 HIS A 905 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8806) covalent geometry : angle 0.61282 (11998) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.24035 ( 2) hydrogen bonds : bond 0.02306 ( 189) hydrogen bonds : angle 4.42654 ( 564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.42 seconds wall clock time: 24 minutes 50.53 seconds (1490.53 seconds total)