Starting phenix.real_space_refine on Tue Apr 29 14:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivd_60925/04_2025/9ivd_60925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivd_60925/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivd_60925/04_2025/9ivd_60925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivd_60925/04_2025/9ivd_60925.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivd_60925/04_2025/9ivd_60925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivd_60925/04_2025/9ivd_60925.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 8, 'ASP:plan': 23, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 48, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 365 Time building chain proxies: 5.47, per 1000 atoms: 0.63 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.13 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: 3.34 Time building geometry restraints manager: 2.83 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 PHE 0.012 0.001 PHE A 829 TYR 0.009 0.001 TYR A 906 ARG 0.007 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.29891 ( 189) hydrogen bonds : angle 9.70147 ( 564) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.34412 ( 2) covalent geometry : bond 0.00414 ( 8806) covalent geometry : angle 0.71878 (11998) *********************** 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 : 0.895 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: 0.2233 time to fit residues: 18.2646 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 : 0.772 ------------------------------------------------------------------------------- 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 97 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.0370 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 977 GLN ** A 950 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 = 0.2992 r_free = 0.2992 target = 0.057333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.046572 restraints weight = 34876.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.048232 restraints weight = 16535.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.049465 restraints weight = 10359.102| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8807 Z= 0.119 Angle : 0.616 14.603 12000 Z= 0.320 Chirality : 0.045 0.164 1424 Planarity : 0.004 0.058 1519 Dihedral : 4.741 33.731 1236 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.57 % Favored : 87.99 % Rotamer: Outliers : 3.36 % Allowed : 27.78 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.23), residues: 1132 helix: -0.98 (0.64), residues: 64 sheet: -1.34 (0.26), residues: 407 loop : -3.34 (0.20), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1016 HIS 0.005 0.001 HIS A 905 PHE 0.009 0.001 PHE A 829 TYR 0.012 0.001 TYR A 906 ARG 0.005 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 189) hydrogen bonds : angle 6.22569 ( 564) SS BOND : bond 0.00263 ( 1) SS BOND : angle 2.08162 ( 2) covalent geometry : bond 0.00273 ( 8806) covalent geometry : angle 0.61571 (11998) *********************** 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 : 1.257 Fit side-chains REVERT: E 289 ASP cc_start: 0.8164 (t0) cc_final: 0.7891 (t0) REVERT: B 176 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 792 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9048 (pp) outliers start: 29 outliers final: 9 residues processed: 83 average time/residue: 0.1744 time to fit residues: 21.7236 Evaluate side-chains 63 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 792 LEU Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2933 r_free = 0.2933 target = 0.055414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.044534 restraints weight = 35756.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.046143 restraints weight = 17193.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.047209 restraints weight = 10832.004| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8807 Z= 0.168 Angle : 0.614 13.757 12000 Z= 0.321 Chirality : 0.045 0.157 1424 Planarity : 0.004 0.056 1519 Dihedral : 4.921 37.249 1234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.90 % Favored : 86.66 % Rotamer: Outliers : 3.82 % Allowed : 28.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1132 helix: -0.78 (0.63), residues: 69 sheet: -1.22 (0.27), residues: 402 loop : -3.25 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 PHE 0.011 0.001 PHE A 829 TYR 0.010 0.001 TYR B1026 ARG 0.002 0.000 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 189) hydrogen bonds : angle 5.46558 ( 564) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.59869 ( 2) covalent geometry : bond 0.00389 ( 8806) covalent geometry : angle 0.61382 (11998) *********************** 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 88 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.984 Fit side-chains REVERT: E 289 ASP cc_start: 0.8461 (t0) cc_final: 0.8109 (t0) REVERT: B 150 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: B 176 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 1041 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7347 (tt) REVERT: A 350 MET cc_start: 0.9599 (ptt) cc_final: 0.9256 (ptp) REVERT: A 1036 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (ptm) outliers start: 33 outliers final: 20 residues processed: 83 average time/residue: 0.1742 time to fit residues: 21.6625 Evaluate side-chains 77 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER 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 947 VAL Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain A residue 19 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 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 873 MET 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 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 27 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** A 950 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 = 0.2955 r_free = 0.2955 target = 0.055907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.045080 restraints weight = 35308.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.046755 restraints weight = 16764.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047967 restraints weight = 10441.646| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1455 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= 0.104 Angle : 0.574 14.002 12000 Z= 0.296 Chirality : 0.045 0.155 1424 Planarity : 0.004 0.057 1519 Dihedral : 4.756 36.149 1234 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.78 % Favored : 88.78 % Rotamer: Outliers : 4.17 % Allowed : 27.20 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.24), residues: 1132 helix: -0.50 (0.65), residues: 69 sheet: -1.14 (0.27), residues: 413 loop : -3.21 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 PHE 0.009 0.001 PHE B 995 TYR 0.008 0.001 TYR B1026 ARG 0.002 0.000 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 189) hydrogen bonds : angle 5.05890 ( 564) SS BOND : bond 0.00183 ( 1) SS BOND : angle 1.43405 ( 2) covalent geometry : bond 0.00242 ( 8806) covalent geometry : angle 0.57331 (11998) *********************** 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 92 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 1.030 Fit side-chains REVERT: E 289 ASP cc_start: 0.8544 (t0) cc_final: 0.8152 (t0) REVERT: B 176 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8485 (p) REVERT: B 974 MET cc_start: 0.8110 (mmm) cc_final: 0.6948 (ttm) REVERT: B 1041 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 350 MET cc_start: 0.9561 (ptt) cc_final: 0.9210 (ptp) REVERT: A 835 MET cc_start: 0.8291 (mtp) cc_final: 0.8066 (mtm) REVERT: A 921 ILE cc_start: 0.5748 (mm) cc_final: 0.5481 (mm) outliers start: 36 outliers final: 18 residues processed: 88 average time/residue: 0.1977 time to fit residues: 25.4920 Evaluate side-chains 73 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER 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 B residue 1041 LEU 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 790 ASN Chi-restraints excluded: chain A residue 866 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 1043 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2896 r_free = 0.2896 target = 0.054919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.044018 restraints weight = 35149.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.045664 restraints weight = 16171.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.046837 restraints weight = 10014.234| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8807 Z= 0.181 Angle : 0.606 14.024 12000 Z= 0.316 Chirality : 0.045 0.155 1424 Planarity : 0.004 0.057 1519 Dihedral : 4.801 35.274 1234 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.16 % Favored : 86.40 % Rotamer: Outliers : 3.70 % Allowed : 28.01 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.24), residues: 1132 helix: -0.73 (0.63), residues: 75 sheet: -1.15 (0.26), residues: 420 loop : -3.20 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1016 HIS 0.005 0.001 HIS A 905 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 TYR B 936 ARG 0.002 0.000 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 189) hydrogen bonds : angle 5.07263 ( 564) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.28011 ( 2) covalent geometry : bond 0.00420 ( 8806) covalent geometry : angle 0.60627 (11998) *********************** 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 84 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.912 Fit side-chains REVERT: E 289 ASP cc_start: 0.8514 (t0) cc_final: 0.8110 (t0) REVERT: E 292 ASP cc_start: 0.9004 (p0) cc_final: 0.8767 (p0) REVERT: B 150 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: B 176 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8467 (p) REVERT: B 896 ASP cc_start: 0.9063 (t0) cc_final: 0.8740 (t0) REVERT: B 957 MET cc_start: 0.9259 (ttp) cc_final: 0.8760 (ttm) REVERT: B 1041 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7339 (tt) REVERT: A 350 MET cc_start: 0.9513 (ptt) cc_final: 0.9145 (ptp) REVERT: A 1036 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (ptm) outliers start: 32 outliers final: 19 residues processed: 80 average time/residue: 0.1719 time to fit residues: 20.5705 Evaluate side-chains 73 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 875 ILE Chi-restraints excluded: chain B residue 895 CYS 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 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 866 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 1036 MET 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 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** A 950 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 = 0.2922 r_free = 0.2922 target = 0.056500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.045325 restraints weight = 35415.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.047002 restraints weight = 15973.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.048220 restraints weight = 9882.587| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8807 Z= 0.109 Angle : 0.585 14.123 12000 Z= 0.299 Chirality : 0.045 0.203 1424 Planarity : 0.004 0.056 1519 Dihedral : 4.722 35.877 1234 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.95 % Favored : 88.60 % Rotamer: Outliers : 3.36 % Allowed : 28.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.24), residues: 1132 helix: -0.21 (0.67), residues: 69 sheet: -0.96 (0.27), residues: 414 loop : -3.11 (0.21), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1016 HIS 0.004 0.001 HIS A 803 PHE 0.009 0.001 PHE B 995 TYR 0.009 0.001 TYR B1026 ARG 0.001 0.000 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.02536 ( 189) hydrogen bonds : angle 4.82361 ( 564) SS BOND : bond 0.00143 ( 1) SS BOND : angle 1.25826 ( 2) covalent geometry : bond 0.00256 ( 8806) covalent geometry : angle 0.58439 (11998) *********************** 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 83 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.965 Fit side-chains REVERT: E 289 ASP cc_start: 0.8508 (t0) cc_final: 0.8087 (t0) REVERT: E 292 ASP cc_start: 0.8983 (p0) cc_final: 0.8759 (p0) REVERT: B 176 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 861 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6511 (mtm-85) REVERT: B 896 ASP cc_start: 0.9008 (t0) cc_final: 0.8753 (t0) REVERT: B 957 MET cc_start: 0.9227 (ttp) cc_final: 0.8738 (ttm) REVERT: B 1041 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7380 (tt) REVERT: A 350 MET cc_start: 0.9488 (ptt) cc_final: 0.9120 (ptp) REVERT: A 1036 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8438 (ptm) outliers start: 29 outliers final: 18 residues processed: 79 average time/residue: 0.1815 time to fit residues: 21.1915 Evaluate side-chains 72 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 176 THR 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 1041 LEU 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 831 VAL Chi-restraints excluded: chain A residue 866 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 1036 MET Chi-restraints excluded: chain A residue 1043 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2899 r_free = 0.2899 target = 0.054853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.043944 restraints weight = 35916.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.045641 restraints weight = 16356.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.046841 restraints weight = 10058.403| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8807 Z= 0.140 Angle : 0.592 13.743 12000 Z= 0.303 Chirality : 0.045 0.193 1424 Planarity : 0.004 0.056 1519 Dihedral : 4.700 35.750 1234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.54 % Favored : 87.01 % Rotamer: Outliers : 3.70 % Allowed : 28.70 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.24), residues: 1132 helix: -0.47 (0.64), residues: 74 sheet: -0.91 (0.27), residues: 414 loop : -3.06 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1016 HIS 0.005 0.001 HIS A 803 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B1026 ARG 0.002 0.000 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.02691 ( 189) hydrogen bonds : angle 4.75747 ( 564) SS BOND : bond 0.00120 ( 1) SS BOND : angle 1.15681 ( 2) covalent geometry : bond 0.00328 ( 8806) covalent geometry : angle 0.59185 (11998) *********************** 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 85 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 1.035 Fit side-chains REVERT: E 289 ASP cc_start: 0.8512 (t0) cc_final: 0.8075 (t0) REVERT: E 292 ASP cc_start: 0.8950 (p0) cc_final: 0.8716 (p0) REVERT: B 176 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 896 ASP cc_start: 0.9059 (t0) cc_final: 0.8786 (t0) REVERT: B 957 MET cc_start: 0.9233 (ttp) cc_final: 0.8718 (ttm) REVERT: B 1041 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7346 (tt) REVERT: A 350 MET cc_start: 0.9464 (ptt) cc_final: 0.9090 (ptp) outliers start: 32 outliers final: 22 residues processed: 81 average time/residue: 0.1841 time to fit residues: 22.2956 Evaluate side-chains 76 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 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 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 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 48 optimal weight: 0.0770 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2943 r_free = 0.2943 target = 0.056362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.045714 restraints weight = 35545.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.047460 restraints weight = 15958.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.048566 restraints weight = 9672.159| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8807 Z= 0.089 Angle : 0.596 14.099 12000 Z= 0.295 Chirality : 0.045 0.179 1424 Planarity : 0.004 0.055 1519 Dihedral : 4.575 36.659 1234 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.51 % Favored : 89.13 % Rotamer: Outliers : 2.66 % Allowed : 29.75 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), residues: 1132 helix: -0.34 (0.65), residues: 74 sheet: -0.81 (0.27), residues: 404 loop : -3.00 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1016 HIS 0.003 0.001 HIS A 261 PHE 0.011 0.001 PHE B 995 TYR 0.008 0.001 TYR B1026 ARG 0.002 0.000 ARG A 739 Details of bonding type rmsd hydrogen bonds : bond 0.02275 ( 189) hydrogen bonds : angle 4.49052 ( 564) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.24704 ( 2) covalent geometry : bond 0.00210 ( 8806) covalent geometry : angle 0.59578 (11998) *********************** 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 86 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.951 Fit side-chains REVERT: E 289 ASP cc_start: 0.8481 (t0) cc_final: 0.8010 (t0) REVERT: E 292 ASP cc_start: 0.8943 (p0) cc_final: 0.8631 (p0) REVERT: B 103 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8958 (t80) REVERT: B 176 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8294 (p) REVERT: B 896 ASP cc_start: 0.8980 (t0) cc_final: 0.8732 (t0) REVERT: B 934 MET cc_start: 0.9127 (tpp) cc_final: 0.8733 (tpp) REVERT: B 957 MET cc_start: 0.9181 (ttp) cc_final: 0.8696 (ttm) REVERT: B 960 LEU cc_start: 0.9387 (mp) cc_final: 0.9127 (mm) REVERT: B 1041 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 1 MET cc_start: 0.8504 (mpp) cc_final: 0.7941 (mpp) outliers start: 23 outliers final: 15 residues processed: 83 average time/residue: 0.1855 time to fit residues: 22.6442 Evaluate side-chains 72 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER 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 1041 LEU Chi-restraints excluded: chain A residue 178 ILE 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 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 880 LEU Chi-restraints excluded: chain A residue 906 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 0.0470 chunk 71 optimal weight: 8.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2891 r_free = 0.2891 target = 0.055312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.044314 restraints weight = 36203.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.045980 restraints weight = 16317.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.047107 restraints weight = 10005.549| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8807 Z= 0.183 Angle : 0.622 13.093 12000 Z= 0.318 Chirality : 0.046 0.359 1424 Planarity : 0.004 0.055 1519 Dihedral : 4.722 36.058 1234 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.63 % Favored : 86.93 % Rotamer: Outliers : 3.24 % Allowed : 29.63 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.24), residues: 1132 helix: -0.20 (0.65), residues: 74 sheet: -0.82 (0.26), residues: 422 loop : -3.16 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1016 HIS 0.006 0.001 HIS A 803 PHE 0.008 0.001 PHE B 995 TYR 0.010 0.001 TYR B1026 ARG 0.007 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 189) hydrogen bonds : angle 4.65608 ( 564) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.94288 ( 2) covalent geometry : bond 0.00427 ( 8806) covalent geometry : angle 0.62179 (11998) *********************** 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 81 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.930 Fit side-chains REVERT: E 289 ASP cc_start: 0.8460 (t0) cc_final: 0.7974 (t0) REVERT: E 292 ASP cc_start: 0.8951 (p0) cc_final: 0.8609 (p0) REVERT: B 150 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: B 176 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 883 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9205 (tt) REVERT: B 896 ASP cc_start: 0.9084 (t0) cc_final: 0.8851 (t0) REVERT: B 934 MET cc_start: 0.8834 (tpp) cc_final: 0.8583 (tpp) REVERT: B 960 LEU cc_start: 0.9400 (mp) cc_final: 0.9163 (mm) REVERT: B 1041 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7329 (tt) outliers start: 28 outliers final: 21 residues processed: 78 average time/residue: 0.1888 time to fit residues: 22.4037 Evaluate side-chains 78 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 883 LEU Chi-restraints excluded: chain B residue 895 CYS 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 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 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 31 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2911 r_free = 0.2911 target = 0.056077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.045166 restraints weight = 35952.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.046842 restraints weight = 15825.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.047990 restraints weight = 9709.333| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8807 Z= 0.128 Angle : 0.617 13.604 12000 Z= 0.309 Chirality : 0.046 0.304 1424 Planarity : 0.004 0.053 1519 Dihedral : 4.738 37.823 1234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.48 % Favored : 88.16 % Rotamer: Outliers : 2.78 % Allowed : 30.21 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1132 helix: -0.04 (0.66), residues: 74 sheet: -0.74 (0.26), residues: 426 loop : -3.16 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 PHE 0.011 0.001 PHE B 995 TYR 0.009 0.001 TYR B1026 ARG 0.007 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02532 ( 189) hydrogen bonds : angle 4.50823 ( 564) SS BOND : bond 0.00109 ( 1) SS BOND : angle 1.11571 ( 2) covalent geometry : bond 0.00303 ( 8806) covalent geometry : angle 0.61688 (11998) ********************** 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 77 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.971 Fit side-chains REVERT: E 289 ASP cc_start: 0.8490 (t0) cc_final: 0.8008 (t0) REVERT: E 292 ASP cc_start: 0.8955 (p0) cc_final: 0.8607 (p0) REVERT: B 176 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 896 ASP cc_start: 0.9069 (t0) cc_final: 0.8860 (t0) REVERT: B 934 MET cc_start: 0.8970 (tpp) cc_final: 0.8697 (tpp) REVERT: B 960 LEU cc_start: 0.9417 (mp) cc_final: 0.9136 (mm) REVERT: B 1041 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7404 (tt) outliers start: 24 outliers final: 20 residues processed: 74 average time/residue: 0.1720 time to fit residues: 20.0990 Evaluate side-chains 75 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 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 B residue 1041 LEU Chi-restraints excluded: chain A residue 29 LEU 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 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 90 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** ** A 950 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 = 0.2893 r_free = 0.2893 target = 0.054309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.043680 restraints weight = 36050.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.045307 restraints weight = 16218.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.046481 restraints weight = 10085.301| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2243 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= 0.147 Angle : 0.601 12.840 12000 Z= 0.306 Chirality : 0.046 0.304 1424 Planarity : 0.004 0.055 1519 Dihedral : 4.753 38.467 1234 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.63 % Favored : 87.01 % Rotamer: Outliers : 3.36 % Allowed : 29.51 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1132 helix: -0.02 (0.66), residues: 74 sheet: -0.75 (0.26), residues: 426 loop : -3.16 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1016 HIS 0.004 0.001 HIS A 905 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B1026 ARG 0.007 0.000 ARG B1015 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 189) hydrogen bonds : angle 4.53458 ( 564) SS BOND : bond 0.00108 ( 1) SS BOND : angle 1.01575 ( 2) covalent geometry : bond 0.00347 ( 8806) covalent geometry : angle 0.60122 (11998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.15 seconds wall clock time: 52 minutes 31.65 seconds (3151.65 seconds total)