Starting phenix.real_space_refine on Sun Aug 24 04:11:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as8_15609/08_2025/8as8_15609.map" } resolution = 3.0 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 10424 2.51 5 N 3060 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16700 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4735 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 14, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4044 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 15, 'TRANS': 482} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.23 Number of scatterers: 16700 At special positions: 0 Unit cell: (131.261, 137.069, 159.139, 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 32 16.00 P 4 15.00 O 3180 8.00 N 3060 7.00 C 10424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 779.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3910 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 61.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.590A pdb=" N SER A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 6' Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.684A pdb=" N MET A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 175 removed outlier: 8.383A pdb=" N THR A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.667A pdb=" N TYR A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.959A pdb=" N PHE A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 233 through 283 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 783 through 807 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.639A pdb=" N GLU A 814 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 835 removed outlier: 3.616A pdb=" N TYR A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.621A pdb=" N GLU A 839 " --> pdb=" O GLU A 835 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 882 removed outlier: 3.712A pdb=" N GLU A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 Processing helix chain 'A' and resid 924 through 944 Processing helix chain 'A' and resid 947 through 955 Processing helix chain 'A' and resid 956 through 959 removed outlier: 3.650A pdb=" N ARG A 959 " --> pdb=" O PRO A 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 985 through 1006 Processing helix chain 'A' and resid 1028 through 1042 removed outlier: 3.678A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.430A pdb=" N LYS B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.580A pdb=" N LEU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.579A pdb=" N TYR B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 175 removed outlier: 8.688A pdb=" N THR B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.613A pdb=" N TYR B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.784A pdb=" N PHE B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 231 through 283 removed outlier: 3.585A pdb=" N ALA B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Proline residue: B 264 - end of helix removed outlier: 3.517A pdb=" N GLN B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 808 removed outlier: 4.012A pdb=" N GLU B 789 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 821 through 835 Processing helix chain 'B' and resid 835 through 851 Processing helix chain 'B' and resid 856 through 884 removed outlier: 3.779A pdb=" N VAL B 884 " --> pdb=" O THR B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 removed outlier: 3.639A pdb=" N ARG B 905 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 944 Processing helix chain 'B' and resid 947 through 955 Processing helix chain 'B' and resid 956 through 959 Processing helix chain 'B' and resid 986 through 1006 Processing helix chain 'B' and resid 1028 through 1042 removed outlier: 3.737A pdb=" N ARG B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1061 Processing helix chain 'C' and resid 45 through 59 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.564A pdb=" N GLU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.709A pdb=" N LEU C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 3.902A pdb=" N TYR C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'D' and resid 45 through 59 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 126 through 148 Processing helix chain 'D' and resid 158 through 170 Proline residue: D 163 - end of helix removed outlier: 3.811A pdb=" N TYR D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.957A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.962A pdb=" N ARG E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 27 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.586A pdb=" N VAL E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 91 Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.044A pdb=" N ASP E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 144 Processing helix chain 'E' and resid 146 through 170 removed outlier: 3.630A pdb=" N ARG E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 220 Processing helix chain 'E' and resid 224 through 232 removed outlier: 5.503A pdb=" N ARG E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 256 removed outlier: 3.514A pdb=" N GLN E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 273 through 280 removed outlier: 4.218A pdb=" N SER E 277 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 290 through 318 Processing helix chain 'E' and resid 321 through 339 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 398 through 406 removed outlier: 3.706A pdb=" N TRP E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 425 Processing helix chain 'E' and resid 429 through 437 Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.622A pdb=" N VAL E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.029A pdb=" N GLY A 28 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 21 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS A 30 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A 19 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 32 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 17 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU A 15 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU A 115 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 17 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP A 23 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 11.388A pdb=" N VAL A 107 " --> pdb=" O TRP A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1017 through 1021 removed outlier: 6.703A pdb=" N ALA A 40 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL A1068 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 42 " --> pdb=" O VAL A1068 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG A1070 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.754A pdb=" N GLY B 28 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU B 15 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU B 115 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 23 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N VAL B 107 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1017 through 1020 removed outlier: 3.565A pdb=" N LEU B1020 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B1049 " --> pdb=" O LEU B1020 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 39 " --> pdb=" O PHE B1048 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR B1050 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 41 " --> pdb=" O THR B1050 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA B 40 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B1068 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 42 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ARG B1070 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B1081 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 893 through 895 removed outlier: 4.014A pdb=" N ALA B 963 " --> pdb=" O ASP B 895 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 966 " --> pdb=" O ILE B 975 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.515A pdb=" N TYR D 101 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.213A pdb=" N GLN D 123 " --> pdb=" O ARG E 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.568A pdb=" N ALA D 154 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'E' and resid 461 through 465 1004 hydrogen bonds defined for protein. 2937 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: 3.26 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5684 1.34 - 1.45: 1744 1.45 - 1.57: 9494 1.57 - 1.69: 7 1.69 - 1.81: 57 Bond restraints: 16986 Sorted by residual: bond pdb=" C4 ADP B1101 " pdb=" C5 ADP B1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A1101 " pdb=" C5 ADP A1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5 ADP B1101 " pdb=" C6 ADP B1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP A1101 " pdb=" C6 ADP A1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N ASP B1021 " pdb=" CA ASP B1021 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.79e+00 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22688 2.32 - 4.65: 248 4.65 - 6.97: 27 6.97 - 9.29: 16 9.29 - 11.62: 3 Bond angle restraints: 22982 Sorted by residual: angle pdb=" CA PRO A 888 " pdb=" N PRO A 888 " pdb=" CD PRO A 888 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 angle pdb=" C GLU B 95 " pdb=" CA GLU B 95 " pdb=" CB GLU B 95 " ideal model delta sigma weight residual 117.23 110.41 6.82 1.36e+00 5.41e-01 2.52e+01 angle pdb=" C GLN C 112 " pdb=" CA GLN C 112 " pdb=" CB GLN C 112 " ideal model delta sigma weight residual 117.23 110.98 6.25 1.36e+00 5.41e-01 2.11e+01 angle pdb=" N PRO A 888 " pdb=" CD PRO A 888 " pdb=" CG PRO A 888 " ideal model delta sigma weight residual 103.20 96.92 6.28 1.50e+00 4.44e-01 1.76e+01 angle pdb=" CA ASP B1021 " pdb=" C ASP B1021 " pdb=" O ASP B1021 " ideal model delta sigma weight residual 121.56 117.08 4.48 1.09e+00 8.42e-01 1.69e+01 ... (remaining 22977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.70: 9671 32.70 - 65.39: 601 65.39 - 98.09: 57 98.09 - 130.79: 1 130.79 - 163.48: 2 Dihedral angle restraints: 10332 sinusoidal: 4307 harmonic: 6025 Sorted by residual: dihedral pdb=" C5' ADP A1101 " pdb=" O5' ADP A1101 " pdb=" PA ADP A1101 " pdb=" O2A ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 136.52 163.48 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1101 " pdb=" O3A ADP A1101 " pdb=" PB ADP A1101 " pdb=" PA ADP A1101 " ideal model delta sinusoidal sigma weight residual 300.00 166.40 133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" C4' ADP B1101 " pdb=" C5' ADP B1101 " pdb=" O5' ADP B1101 " pdb=" PA ADP B1101 " ideal model delta sinusoidal sigma weight residual -180.00 -64.22 -115.78 1 2.00e+01 2.50e-03 3.44e+01 ... (remaining 10329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1929 0.038 - 0.075: 470 0.075 - 0.113: 151 0.113 - 0.150: 18 0.150 - 0.188: 5 Chirality restraints: 2573 Sorted by residual: chirality pdb=" CA ILE B1049 " pdb=" N ILE B1049 " pdb=" C ILE B1049 " pdb=" CB ILE B1049 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" C3' ADP B1101 " pdb=" C2' ADP B1101 " pdb=" C4' ADP B1101 " pdb=" O3' ADP B1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 2570 not shown) Planarity restraints: 3017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 887 " 0.088 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 888 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 888 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 888 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 982 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLN A 982 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN A 982 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 983 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1020 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C LEU B1020 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B1020 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B1021 " 0.011 2.00e-02 2.50e+03 ... (remaining 3014 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 162 2.54 - 3.13: 14001 3.13 - 3.72: 27395 3.72 - 4.31: 36219 4.31 - 4.90: 60616 Nonbonded interactions: 138393 Sorted by model distance: nonbonded pdb=" O ASN D 126 " pdb=" OG SER D 130 " model vdw 1.950 3.040 nonbonded pdb=" OG SER A 971 " pdb=" OD1 ASN A 973 " model vdw 1.978 3.040 nonbonded pdb=" O LEU B1058 " pdb=" OG1 THR B1062 " model vdw 1.989 3.040 nonbonded pdb=" OG SER E 44 " pdb=" OD1 ASP E 46 " model vdw 2.003 3.040 nonbonded pdb=" OG SER B 216 " pdb=" OD1 ASP B 218 " model vdw 2.017 3.040 ... (remaining 138388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.790 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 0.131 16986 Z= 0.221 Angle : 0.618 11.617 22982 Z= 0.347 Chirality : 0.038 0.188 2573 Planarity : 0.004 0.128 3017 Dihedral : 19.614 163.482 6422 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 4.10 % Allowed : 36.76 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 2068 helix: 1.98 (0.16), residues: 1187 sheet: -0.91 (0.34), residues: 238 loop : -1.50 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 308 TYR 0.013 0.001 TYR B 891 PHE 0.011 0.001 PHE B 919 TRP 0.024 0.001 TRP B 128 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00413 (16986) covalent geometry : angle 0.61835 (22982) hydrogen bonds : bond 0.13052 ( 1004) hydrogen bonds : angle 5.92831 ( 2937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (m) REVERT: A 907 LEU cc_start: 0.9083 (tp) cc_final: 0.8849 (tp) REVERT: B 967 MET cc_start: 0.7760 (mtp) cc_final: 0.7558 (mtp) REVERT: E 51 GLU cc_start: 0.8604 (pm20) cc_final: 0.8292 (mp0) outliers start: 73 outliers final: 55 residues processed: 399 average time/residue: 0.6447 time to fit residues: 284.1322 Evaluate side-chains 380 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 324 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 485 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 232 GLN D 68 ASN E 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096832 restraints weight = 25268.716| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.76 r_work: 0.2959 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16986 Z= 0.191 Angle : 0.683 12.792 22982 Z= 0.340 Chirality : 0.042 0.178 2573 Planarity : 0.004 0.059 3017 Dihedral : 9.253 177.957 2423 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.75 % Favored : 94.00 % Rotamer: Outliers : 6.13 % Allowed : 30.24 % Favored : 63.63 % 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: 0.97 (0.19), residues: 2068 helix: 2.04 (0.15), residues: 1194 sheet: -0.71 (0.34), residues: 222 loop : -1.58 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 282 TYR 0.021 0.002 TYR B 891 PHE 0.016 0.002 PHE B 886 TRP 0.020 0.001 TRP B 128 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00439 (16986) covalent geometry : angle 0.68334 (22982) hydrogen bonds : bond 0.04691 ( 1004) hydrogen bonds : angle 4.74327 ( 2937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 370 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9077 (ttp) cc_final: 0.8838 (ttm) REVERT: A 792 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8854 (mtm110) REVERT: A 813 VAL cc_start: 0.8331 (p) cc_final: 0.8050 (m) REVERT: A 925 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8541 (tp30) REVERT: B 115 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 193 ASP cc_start: 0.8793 (t0) cc_final: 0.8524 (t0) REVERT: B 227 ASP cc_start: 0.8033 (p0) cc_final: 0.7541 (p0) REVERT: B 796 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: B 803 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: B 847 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: B 849 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 876 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 901 HIS cc_start: 0.8304 (t-90) cc_final: 0.7956 (t-90) REVERT: B 1020 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B 1060 ASP cc_start: 0.8195 (m-30) cc_final: 0.7988 (m-30) REVERT: B 1083 GLU cc_start: 0.8545 (pp20) cc_final: 0.7873 (tm-30) REVERT: D 54 GLU cc_start: 0.8579 (tp30) cc_final: 0.8369 (tp30) REVERT: D 79 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: D 112 GLN cc_start: 0.5506 (OUTLIER) cc_final: 0.5230 (tp40) REVERT: E 142 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6585 (tmt170) REVERT: E 143 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7359 (mt) REVERT: E 163 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8282 (mtp-110) REVERT: E 166 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: E 167 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: E 327 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8192 (tpt90) REVERT: E 386 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7860 (t70) REVERT: E 400 ASP cc_start: 0.8673 (p0) cc_final: 0.8436 (p0) REVERT: E 403 ASP cc_start: 0.8815 (m-30) cc_final: 0.8543 (m-30) outliers start: 109 outliers final: 45 residues processed: 437 average time/residue: 0.6768 time to fit residues: 326.2253 Evaluate side-chains 390 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 201 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN B 901 HIS C 232 GLN E 119 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095679 restraints weight = 25689.374| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.78 r_work: 0.2952 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16986 Z= 0.192 Angle : 0.672 12.778 22982 Z= 0.333 Chirality : 0.042 0.180 2573 Planarity : 0.004 0.058 3017 Dihedral : 7.909 166.621 2357 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.51 % Favored : 94.29 % Rotamer: Outliers : 6.97 % Allowed : 30.24 % Favored : 62.79 % 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: 0.92 (0.19), residues: 2068 helix: 1.99 (0.15), residues: 1199 sheet: -0.77 (0.33), residues: 222 loop : -1.59 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 282 TYR 0.022 0.001 TYR B 891 PHE 0.019 0.002 PHE A 221 TRP 0.022 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00449 (16986) covalent geometry : angle 0.67181 (22982) hydrogen bonds : bond 0.04450 ( 1004) hydrogen bonds : angle 4.55709 ( 2937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 382 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 803 GLU cc_start: 0.8419 (tp30) cc_final: 0.8155 (tp30) REVERT: A 813 VAL cc_start: 0.8333 (p) cc_final: 0.8063 (m) REVERT: A 827 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 905 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7686 (ptp90) REVERT: A 925 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8492 (tp30) REVERT: A 948 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8507 (tm) REVERT: A 1026 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8862 (mtm-85) REVERT: B 79 ASP cc_start: 0.8831 (p0) cc_final: 0.8602 (p0) REVERT: B 115 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 171 MET cc_start: 0.8202 (ptm) cc_final: 0.7948 (ptm) REVERT: B 192 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: B 193 ASP cc_start: 0.8795 (t0) cc_final: 0.8593 (t0) REVERT: B 219 GLU cc_start: 0.8680 (mp0) cc_final: 0.8367 (mp0) REVERT: B 227 ASP cc_start: 0.8059 (p0) cc_final: 0.7697 (p0) REVERT: B 796 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: B 803 GLU cc_start: 0.8236 (mp0) cc_final: 0.8012 (mp0) REVERT: B 847 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: B 849 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8146 (t0) REVERT: B 876 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 909 LYS cc_start: 0.8363 (ptpp) cc_final: 0.8129 (ptpp) REVERT: B 978 ARG cc_start: 0.2824 (OUTLIER) cc_final: 0.0281 (ttt180) REVERT: B 1020 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 1060 ASP cc_start: 0.8144 (m-30) cc_final: 0.7870 (m-30) REVERT: B 1083 GLU cc_start: 0.8548 (pp20) cc_final: 0.7850 (tm-30) REVERT: D 54 GLU cc_start: 0.8627 (tp30) cc_final: 0.8372 (tp30) REVERT: D 79 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: D 112 GLN cc_start: 0.5387 (OUTLIER) cc_final: 0.5053 (tp40) REVERT: E 142 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6722 (tmt170) REVERT: E 143 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7248 (mt) REVERT: E 163 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8378 (mtp-110) REVERT: E 167 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8129 (OUTLIER) REVERT: E 327 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8237 (tpt90) REVERT: E 386 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7934 (t70) REVERT: E 403 ASP cc_start: 0.8832 (m-30) cc_final: 0.8568 (m-30) outliers start: 124 outliers final: 53 residues processed: 453 average time/residue: 0.6446 time to fit residues: 322.1574 Evaluate side-chains 407 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 339 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1026 ARG Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 847 TYR Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 164 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN B 258 GLN B 794 ASN C 232 GLN E 119 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.096031 restraints weight = 25626.664| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.79 r_work: 0.2948 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16986 Z= 0.191 Angle : 0.664 12.130 22982 Z= 0.329 Chirality : 0.042 0.190 2573 Planarity : 0.004 0.060 3017 Dihedral : 7.430 150.389 2347 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 7.08 % Allowed : 30.30 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.19), residues: 2068 helix: 1.97 (0.15), residues: 1199 sheet: -0.78 (0.34), residues: 222 loop : -1.58 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 792 TYR 0.021 0.001 TYR B 891 PHE 0.012 0.002 PHE A 242 TRP 0.024 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00447 (16986) covalent geometry : angle 0.66359 (22982) hydrogen bonds : bond 0.04340 ( 1004) hydrogen bonds : angle 4.50465 ( 2937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 361 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 803 GLU cc_start: 0.8457 (tp30) cc_final: 0.7964 (tp30) REVERT: A 813 VAL cc_start: 0.8298 (p) cc_final: 0.8024 (m) REVERT: A 827 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 905 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7689 (ptp90) REVERT: A 948 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8512 (tm) REVERT: A 1026 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8900 (mtm-85) REVERT: B 19 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 79 ASP cc_start: 0.8832 (p0) cc_final: 0.8592 (p0) REVERT: B 115 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 171 MET cc_start: 0.8228 (ptm) cc_final: 0.7919 (ptm) REVERT: B 192 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: B 193 ASP cc_start: 0.8789 (t0) cc_final: 0.8543 (t0) REVERT: B 220 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 250 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8497 (pp30) REVERT: B 796 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: B 803 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: B 849 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8172 (t0) REVERT: B 872 GLU cc_start: 0.8605 (pp20) cc_final: 0.8388 (pp20) REVERT: B 876 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 909 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8105 (ptpp) REVERT: B 978 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.0298 (ttt180) REVERT: B 1020 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8112 (pp) REVERT: B 1060 ASP cc_start: 0.8221 (m-30) cc_final: 0.7950 (m-30) REVERT: B 1083 GLU cc_start: 0.8566 (pp20) cc_final: 0.7866 (tm-30) REVERT: D 54 GLU cc_start: 0.8674 (tp30) cc_final: 0.8383 (tp30) REVERT: D 79 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: D 112 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.5173 (tp40) REVERT: E 142 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6653 (tmt170) REVERT: E 143 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7115 (mt) REVERT: E 163 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8406 (mtp-110) REVERT: E 167 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8118 (OUTLIER) REVERT: E 327 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8250 (tpt90) REVERT: E 386 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (t70) REVERT: E 403 ASP cc_start: 0.8835 (m-30) cc_final: 0.8576 (m-30) REVERT: E 421 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 126 outliers final: 53 residues processed: 435 average time/residue: 0.6607 time to fit residues: 317.3985 Evaluate side-chains 407 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 335 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1026 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 909 LYS Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 200 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 232 GLN E 119 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096335 restraints weight = 25352.389| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.77 r_work: 0.2956 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16986 Z= 0.182 Angle : 0.668 11.376 22982 Z= 0.329 Chirality : 0.042 0.349 2573 Planarity : 0.004 0.061 3017 Dihedral : 7.227 134.949 2343 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.80 % Favored : 94.05 % Rotamer: Outliers : 6.63 % Allowed : 31.31 % Favored : 62.06 % 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: 0.93 (0.19), residues: 2068 helix: 1.98 (0.15), residues: 1199 sheet: -0.67 (0.34), residues: 220 loop : -1.57 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 792 TYR 0.022 0.002 TYR A 825 PHE 0.012 0.001 PHE A 242 TRP 0.025 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00421 (16986) covalent geometry : angle 0.66772 (22982) hydrogen bonds : bond 0.04289 ( 1004) hydrogen bonds : angle 4.43653 ( 2937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 365 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 803 GLU cc_start: 0.8457 (tp30) cc_final: 0.7975 (tp30) REVERT: A 813 VAL cc_start: 0.8282 (p) cc_final: 0.8011 (m) REVERT: A 827 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8353 (tm-30) REVERT: A 905 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7693 (ptp90) REVERT: A 940 ASP cc_start: 0.8510 (t0) cc_final: 0.8309 (t0) REVERT: A 948 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8530 (tm) REVERT: A 1026 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8893 (mtm-85) REVERT: B 19 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 79 ASP cc_start: 0.8827 (p0) cc_final: 0.8563 (p0) REVERT: B 115 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 171 MET cc_start: 0.8244 (ptm) cc_final: 0.7920 (ptm) REVERT: B 193 ASP cc_start: 0.8791 (t0) cc_final: 0.8555 (t0) REVERT: B 247 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8497 (pp20) REVERT: B 796 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: B 803 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: B 849 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8086 (t0) REVERT: B 876 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8018 (mm-30) REVERT: B 967 MET cc_start: 0.8009 (mtp) cc_final: 0.7529 (mtt) REVERT: B 978 ARG cc_start: 0.2462 (OUTLIER) cc_final: 0.0018 (ttt180) REVERT: B 1020 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 1060 ASP cc_start: 0.8261 (m-30) cc_final: 0.7953 (m-30) REVERT: B 1083 GLU cc_start: 0.8553 (pp20) cc_final: 0.7889 (tm-30) REVERT: D 54 GLU cc_start: 0.8673 (tp30) cc_final: 0.8421 (tp30) REVERT: D 60 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9193 (pt) REVERT: D 79 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: D 112 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.5162 (tp40) REVERT: E 28 ARG cc_start: 0.8901 (mtp-110) cc_final: 0.8379 (mtp-110) REVERT: E 142 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6591 (tmt170) REVERT: E 143 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7109 (mt) REVERT: E 163 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8402 (mtp-110) REVERT: E 295 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8758 (tp) REVERT: E 327 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8252 (tpt90) REVERT: E 386 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7944 (t70) REVERT: E 403 ASP cc_start: 0.8841 (m-30) cc_final: 0.8549 (m-30) REVERT: E 421 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8431 (mp) outliers start: 118 outliers final: 58 residues processed: 433 average time/residue: 0.5963 time to fit residues: 286.4004 Evaluate side-chains 418 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1026 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 169 optimal weight: 0.0980 chunk 150 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN B1073 GLN C 232 GLN E 119 ASN E 251 GLN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097180 restraints weight = 25361.844| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.80 r_work: 0.2978 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16986 Z= 0.146 Angle : 0.661 12.643 22982 Z= 0.324 Chirality : 0.042 0.256 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.937 117.413 2338 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 6.86 % Allowed : 30.80 % Favored : 62.34 % 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: 0.99 (0.19), residues: 2068 helix: 2.06 (0.15), residues: 1198 sheet: -1.05 (0.32), residues: 250 loop : -1.43 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 282 TYR 0.020 0.001 TYR B 891 PHE 0.012 0.001 PHE A 242 TRP 0.027 0.001 TRP B 128 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00335 (16986) covalent geometry : angle 0.66128 (22982) hydrogen bonds : bond 0.04061 ( 1004) hydrogen bonds : angle 4.35182 ( 2937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 378 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4161 (OUTLIER) cc_final: 0.3637 (mm) REVERT: A 272 TYR cc_start: 0.8851 (t80) cc_final: 0.8600 (t80) REVERT: A 792 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8822 (ttp80) REVERT: A 803 GLU cc_start: 0.8442 (tp30) cc_final: 0.7924 (tp30) REVERT: A 813 VAL cc_start: 0.8229 (p) cc_final: 0.7967 (m) REVERT: A 827 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 907 LEU cc_start: 0.9061 (tp) cc_final: 0.8846 (tp) REVERT: A 937 GLN cc_start: 0.8460 (tt0) cc_final: 0.8237 (mt0) REVERT: A 948 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8517 (tm) REVERT: B 19 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 79 ASP cc_start: 0.8814 (p0) cc_final: 0.8515 (p0) REVERT: B 115 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 171 MET cc_start: 0.8330 (ptm) cc_final: 0.8030 (ptm) REVERT: B 192 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7916 (mmm-85) REVERT: B 193 ASP cc_start: 0.8786 (t0) cc_final: 0.8552 (t0) REVERT: B 247 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8511 (pp20) REVERT: B 796 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7838 (tp30) REVERT: B 803 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 849 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8046 (t0) REVERT: B 872 GLU cc_start: 0.8607 (pp20) cc_final: 0.8370 (pp20) REVERT: B 876 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 909 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8489 (tttp) REVERT: B 967 MET cc_start: 0.8060 (mtp) cc_final: 0.7610 (mtt) REVERT: B 978 ARG cc_start: 0.2500 (OUTLIER) cc_final: 0.0067 (ttt180) REVERT: B 1020 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 1060 ASP cc_start: 0.8243 (m-30) cc_final: 0.7948 (m-30) REVERT: B 1083 GLU cc_start: 0.8532 (pp20) cc_final: 0.7902 (tm-30) REVERT: D 54 GLU cc_start: 0.8658 (tp30) cc_final: 0.8380 (tp30) REVERT: D 112 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.5210 (tp40) REVERT: E 80 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7503 (tp-100) REVERT: E 143 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7150 (mt) REVERT: E 167 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: E 295 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8709 (tp) REVERT: E 327 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8228 (tpt90) REVERT: E 386 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7922 (t70) REVERT: E 399 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: E 403 ASP cc_start: 0.8804 (m-30) cc_final: 0.8547 (m-30) REVERT: E 421 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8392 (mp) outliers start: 122 outliers final: 58 residues processed: 452 average time/residue: 0.5951 time to fit residues: 299.1638 Evaluate side-chains 414 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 978 ARG Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 50 optimal weight: 1.9990 chunk 162 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 175 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 250 GLN C 232 GLN E 119 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097311 restraints weight = 25347.567| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.78 r_work: 0.2973 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16986 Z= 0.158 Angle : 0.685 12.421 22982 Z= 0.335 Chirality : 0.042 0.284 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.763 117.382 2335 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 6.07 % Allowed : 32.49 % Favored : 61.44 % 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: 1.00 (0.19), residues: 2068 helix: 2.05 (0.15), residues: 1196 sheet: -1.04 (0.32), residues: 252 loop : -1.40 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 163 TYR 0.021 0.001 TYR A 891 PHE 0.028 0.001 PHE A 221 TRP 0.025 0.001 TRP B 128 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00368 (16986) covalent geometry : angle 0.68451 (22982) hydrogen bonds : bond 0.04079 ( 1004) hydrogen bonds : angle 4.37509 ( 2937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 359 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3641 (mm) REVERT: A 139 MET cc_start: 0.9090 (ttp) cc_final: 0.8813 (ttm) REVERT: A 803 GLU cc_start: 0.8519 (tp30) cc_final: 0.8175 (tp30) REVERT: A 813 VAL cc_start: 0.8202 (p) cc_final: 0.7946 (m) REVERT: A 827 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 937 GLN cc_start: 0.8461 (tt0) cc_final: 0.8235 (mt0) REVERT: A 948 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8528 (tm) REVERT: A 1026 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8950 (mmm-85) REVERT: B 19 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 79 ASP cc_start: 0.8807 (p0) cc_final: 0.8490 (p0) REVERT: B 115 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 171 MET cc_start: 0.8335 (ptm) cc_final: 0.7997 (ptm) REVERT: B 192 ARG cc_start: 0.8309 (mpp80) cc_final: 0.7959 (mtm180) REVERT: B 193 ASP cc_start: 0.8824 (t0) cc_final: 0.8594 (t0) REVERT: B 238 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 247 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: B 784 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7889 (pp20) REVERT: B 803 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 806 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8077 (ttm-80) REVERT: B 872 GLU cc_start: 0.8642 (pp20) cc_final: 0.8407 (pp20) REVERT: B 876 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8103 (mm-30) REVERT: B 967 MET cc_start: 0.7954 (mtp) cc_final: 0.7750 (mtp) REVERT: B 1020 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 1060 ASP cc_start: 0.8285 (m-30) cc_final: 0.7979 (m-30) REVERT: B 1083 GLU cc_start: 0.8471 (pp20) cc_final: 0.7815 (tm-30) REVERT: D 54 GLU cc_start: 0.8653 (tp30) cc_final: 0.8438 (tp30) REVERT: D 60 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9196 (pt) REVERT: D 112 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.5229 (tp40) REVERT: E 1 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4559 (pmm) REVERT: E 80 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7495 (tp-100) REVERT: E 130 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8240 (p) REVERT: E 143 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7159 (mt) REVERT: E 163 ARG cc_start: 0.8695 (mtp-110) cc_final: 0.8407 (ttm110) REVERT: E 167 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: E 277 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8681 (m) REVERT: E 295 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8717 (tp) REVERT: E 327 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8215 (tpt90) REVERT: E 352 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: E 386 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7813 (t70) REVERT: E 399 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: E 403 ASP cc_start: 0.8813 (m-30) cc_final: 0.8520 (m-30) REVERT: E 421 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8390 (mp) REVERT: E 461 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8611 (pp) outliers start: 108 outliers final: 54 residues processed: 425 average time/residue: 0.5652 time to fit residues: 266.5088 Evaluate side-chains 415 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 340 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN B1029 HIS C 232 GLN E 119 ASN E 441 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096810 restraints weight = 25452.455| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.79 r_work: 0.2972 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16986 Z= 0.174 Angle : 0.692 12.448 22982 Z= 0.339 Chirality : 0.043 0.356 2573 Planarity : 0.004 0.062 3017 Dihedral : 6.603 117.326 2331 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 5.85 % Allowed : 32.60 % Favored : 61.55 % 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: 0.98 (0.19), residues: 2068 helix: 2.02 (0.15), residues: 1197 sheet: -0.96 (0.33), residues: 242 loop : -1.39 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 410 TYR 0.048 0.002 TYR A 891 PHE 0.013 0.001 PHE A 242 TRP 0.027 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00407 (16986) covalent geometry : angle 0.69168 (22982) hydrogen bonds : bond 0.04150 ( 1004) hydrogen bonds : angle 4.39112 ( 2937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 353 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3878 (OUTLIER) cc_final: 0.3368 (mm) REVERT: A 139 MET cc_start: 0.9079 (ttp) cc_final: 0.8800 (ttm) REVERT: A 803 GLU cc_start: 0.8593 (tp30) cc_final: 0.8111 (tp30) REVERT: A 813 VAL cc_start: 0.8192 (p) cc_final: 0.7930 (m) REVERT: A 827 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 948 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8569 (tm) REVERT: A 1026 ARG cc_start: 0.9152 (mtm-85) cc_final: 0.8900 (mmm-85) REVERT: B 17 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8355 (ttt90) REVERT: B 19 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7849 (mm-30) REVERT: B 79 ASP cc_start: 0.8790 (p0) cc_final: 0.8465 (p0) REVERT: B 115 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 171 MET cc_start: 0.8309 (ptm) cc_final: 0.7955 (ptm) REVERT: B 192 ARG cc_start: 0.8311 (mpp80) cc_final: 0.7987 (mtm180) REVERT: B 193 ASP cc_start: 0.8859 (t0) cc_final: 0.8609 (t0) REVERT: B 247 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8473 (pp20) REVERT: B 784 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7842 (pp20) REVERT: B 803 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 806 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8112 (ttm-80) REVERT: B 872 GLU cc_start: 0.8686 (pp20) cc_final: 0.8460 (pp20) REVERT: B 876 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 946 ARG cc_start: 0.7882 (tmm-80) cc_final: 0.7674 (ppp80) REVERT: B 1020 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8159 (pp) REVERT: B 1056 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7706 (ttm-80) REVERT: B 1060 ASP cc_start: 0.8290 (m-30) cc_final: 0.7939 (m-30) REVERT: B 1083 GLU cc_start: 0.8497 (pp20) cc_final: 0.7837 (tm-30) REVERT: D 54 GLU cc_start: 0.8730 (tp30) cc_final: 0.8407 (tp30) REVERT: D 60 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9196 (pt) REVERT: D 112 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5199 (tp40) REVERT: E 1 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.4533 (pmm) REVERT: E 143 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7208 (mt) REVERT: E 163 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8395 (ttm110) REVERT: E 167 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: E 277 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8665 (m) REVERT: E 295 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (tp) REVERT: E 327 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8223 (tpt90) REVERT: E 352 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: E 386 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (t70) REVERT: E 399 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: E 403 ASP cc_start: 0.8811 (m-30) cc_final: 0.8505 (m-30) REVERT: E 461 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8543 (pp) outliers start: 104 outliers final: 58 residues processed: 423 average time/residue: 0.5876 time to fit residues: 275.5528 Evaluate side-chains 411 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 336 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1075 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 187 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN C 232 GLN E 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099890 restraints weight = 25348.565| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.80 r_work: 0.2975 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16986 Z= 0.179 Angle : 0.705 12.370 22982 Z= 0.343 Chirality : 0.043 0.340 2573 Planarity : 0.004 0.062 3017 Dihedral : 6.563 115.676 2331 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 5.23 % Allowed : 33.50 % Favored : 61.27 % 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: 0.93 (0.19), residues: 2068 helix: 1.96 (0.15), residues: 1201 sheet: -0.97 (0.33), residues: 242 loop : -1.42 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 17 TYR 0.043 0.002 TYR A 891 PHE 0.021 0.001 PHE A 221 TRP 0.030 0.001 TRP B 128 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00419 (16986) covalent geometry : angle 0.70472 (22982) hydrogen bonds : bond 0.04202 ( 1004) hydrogen bonds : angle 4.38854 ( 2937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 354 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3891 (OUTLIER) cc_final: 0.3371 (mm) REVERT: A 139 MET cc_start: 0.9046 (ttp) cc_final: 0.8775 (ttm) REVERT: A 792 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8255 (ttp-110) REVERT: A 803 GLU cc_start: 0.8614 (tp30) cc_final: 0.8144 (tp30) REVERT: A 813 VAL cc_start: 0.8184 (p) cc_final: 0.7924 (m) REVERT: A 827 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 858 GLN cc_start: 0.8261 (mp10) cc_final: 0.7995 (mp10) REVERT: A 905 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7709 (ptp90) REVERT: A 948 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8567 (tm) REVERT: A 1026 ARG cc_start: 0.9126 (mtm-85) cc_final: 0.8921 (mmm-85) REVERT: B 17 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8371 (ttt90) REVERT: B 19 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 79 ASP cc_start: 0.8802 (p0) cc_final: 0.8485 (p0) REVERT: B 115 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 171 MET cc_start: 0.8333 (ptm) cc_final: 0.7948 (ptm) REVERT: B 192 ARG cc_start: 0.8306 (mpp80) cc_final: 0.7966 (mtm180) REVERT: B 193 ASP cc_start: 0.8885 (t0) cc_final: 0.8640 (t0) REVERT: B 233 ASP cc_start: 0.8334 (t0) cc_final: 0.8123 (t0) REVERT: B 238 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 784 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7836 (pp20) REVERT: B 803 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 806 ARG cc_start: 0.8474 (tmm-80) cc_final: 0.8130 (ttm-80) REVERT: B 872 GLU cc_start: 0.8690 (pp20) cc_final: 0.8463 (pp20) REVERT: B 876 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 1020 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8156 (pp) REVERT: B 1056 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7680 (ttm-80) REVERT: B 1060 ASP cc_start: 0.8299 (m-30) cc_final: 0.7951 (m-30) REVERT: B 1083 GLU cc_start: 0.8494 (pp20) cc_final: 0.7813 (tm-30) REVERT: C 164 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: D 54 GLU cc_start: 0.8628 (tp30) cc_final: 0.8312 (tp30) REVERT: D 112 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5277 (tp40) REVERT: E 1 MET cc_start: 0.4866 (OUTLIER) cc_final: 0.4539 (pmm) REVERT: E 143 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7176 (mt) REVERT: E 163 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8412 (ttm110) REVERT: E 167 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: E 277 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8665 (m) REVERT: E 295 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8750 (tp) REVERT: E 327 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8183 (tpt90) REVERT: E 352 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: E 386 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7830 (t70) REVERT: E 399 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: E 403 ASP cc_start: 0.8805 (m-30) cc_final: 0.8494 (m-30) REVERT: E 461 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8556 (pp) outliers start: 93 outliers final: 54 residues processed: 412 average time/residue: 0.5917 time to fit residues: 270.0573 Evaluate side-chains 417 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 0.0010 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 0.0770 chunk 156 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099524 restraints weight = 25235.840| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.81 r_work: 0.3014 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16986 Z= 0.134 Angle : 0.703 11.933 22982 Z= 0.341 Chirality : 0.042 0.329 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.332 108.426 2331 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 4.10 % Allowed : 34.91 % Favored : 60.99 % 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: 1.07 (0.19), residues: 2068 helix: 2.08 (0.15), residues: 1199 sheet: -0.96 (0.32), residues: 252 loop : -1.31 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 410 TYR 0.037 0.001 TYR A 891 PHE 0.013 0.001 PHE A 242 TRP 0.032 0.001 TRP B 128 HIS 0.004 0.001 HIS B1061 Details of bonding type rmsd covalent geometry : bond 0.00301 (16986) covalent geometry : angle 0.70292 (22982) hydrogen bonds : bond 0.03859 ( 1004) hydrogen bonds : angle 4.32585 ( 2937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3715 (mm) REVERT: A 139 MET cc_start: 0.9059 (ttp) cc_final: 0.8792 (ttm) REVERT: A 803 GLU cc_start: 0.8622 (tp30) cc_final: 0.8070 (tp30) REVERT: A 813 VAL cc_start: 0.8144 (p) cc_final: 0.7896 (m) REVERT: A 827 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 858 GLN cc_start: 0.8324 (mp10) cc_final: 0.8024 (mp10) REVERT: A 948 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (tm) REVERT: B 17 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8347 (ttt90) REVERT: B 19 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 79 ASP cc_start: 0.8803 (p0) cc_final: 0.8441 (p0) REVERT: B 171 MET cc_start: 0.8332 (ptm) cc_final: 0.8087 (ptm) REVERT: B 192 ARG cc_start: 0.8275 (mpp80) cc_final: 0.7951 (mtm180) REVERT: B 193 ASP cc_start: 0.8875 (t0) cc_final: 0.8627 (t0) REVERT: B 238 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8198 (p) REVERT: B 784 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7812 (pp20) REVERT: B 803 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 806 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.8102 (ttm-80) REVERT: B 872 GLU cc_start: 0.8690 (pp20) cc_final: 0.8459 (pp20) REVERT: B 876 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 946 ARG cc_start: 0.8199 (ppp80) cc_final: 0.7668 (mtm110) REVERT: B 967 MET cc_start: 0.7544 (mtp) cc_final: 0.7276 (mtp) REVERT: B 1020 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8087 (pp) REVERT: B 1056 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.7765 (ttm-80) REVERT: B 1060 ASP cc_start: 0.8256 (m-30) cc_final: 0.7899 (m-30) REVERT: B 1083 GLU cc_start: 0.8382 (pp20) cc_final: 0.7685 (tm-30) REVERT: C 164 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: D 54 GLU cc_start: 0.8621 (tp30) cc_final: 0.8279 (tp30) REVERT: D 112 GLN cc_start: 0.5881 (OUTLIER) cc_final: 0.5272 (tp40) REVERT: E 1 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4463 (pmm) REVERT: E 28 ARG cc_start: 0.8827 (mtp-110) cc_final: 0.8340 (mtp-110) REVERT: E 80 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: E 163 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8410 (ttm110) REVERT: E 167 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: E 220 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7776 (tm-30) REVERT: E 277 SER cc_start: 0.8921 (t) cc_final: 0.8587 (m) REVERT: E 295 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8701 (tp) REVERT: E 327 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8220 (tpt90) REVERT: E 352 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: E 376 GLU cc_start: 0.8113 (pm20) cc_final: 0.7909 (pm20) REVERT: E 386 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7859 (t70) REVERT: E 399 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: E 400 ASP cc_start: 0.8656 (p0) cc_final: 0.8326 (p0) REVERT: E 403 ASP cc_start: 0.8794 (m-30) cc_final: 0.8495 (m-30) REVERT: E 421 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8419 (mp) REVERT: E 461 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8500 (pp) outliers start: 73 outliers final: 46 residues processed: 426 average time/residue: 0.5594 time to fit residues: 264.2791 Evaluate side-chains 419 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 463 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 40 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 overall best weight: 0.4540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 232 GLN E 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098658 restraints weight = 25355.262| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.81 r_work: 0.2995 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16986 Z= 0.152 Angle : 0.710 11.869 22982 Z= 0.346 Chirality : 0.042 0.323 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.192 105.061 2327 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.25 % Rotamer: Outliers : 4.44 % Allowed : 35.24 % Favored : 60.31 % 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: 1.06 (0.19), residues: 2068 helix: 2.07 (0.15), residues: 1196 sheet: -0.93 (0.32), residues: 252 loop : -1.33 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.038 0.002 TYR A 891 PHE 0.013 0.001 PHE A 221 TRP 0.033 0.001 TRP B 128 HIS 0.003 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00353 (16986) covalent geometry : angle 0.71016 (22982) hydrogen bonds : bond 0.03976 ( 1004) hydrogen bonds : angle 4.35022 ( 2937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6286.52 seconds wall clock time: 107 minutes 53.42 seconds (6473.42 seconds total)