Starting phenix.real_space_refine on Sun Jun 15 03:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8as8_15609/06_2025/8as8_15609_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as8_15609/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8as8_15609/06_2025/8as8_15609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as8_15609/06_2025/8as8_15609.map" model { file = "/net/cci-nas-00/data/ceres_data/8as8_15609/06_2025/8as8_15609_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as8_15609/06_2025/8as8_15609_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.67, per 1000 atoms: 0.58 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: 4.00 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.60 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: 5.17 Time building geometry restraints manager: 4.75 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: 7.110 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.670 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.580 ------------------------------------------------------------------------------- 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 : 32.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (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 TRP 0.024 0.001 TRP B 128 HIS 0.004 0.001 HIS E 330 PHE 0.011 0.001 PHE B 919 TYR 0.013 0.001 TYR B 891 ARG 0.010 0.000 ARG E 308 Details of bonding type rmsd hydrogen bonds : bond 0.13052 ( 1004) hydrogen bonds : angle 5.92831 ( 2937) covalent geometry : bond 0.00413 (16986) covalent geometry : angle 0.61835 (22982) *********************** 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 : 1.791 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: 1.2784 time to fit residues: 566.4259 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 : 1.770 ------------------------------------------------------------------------------- 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 173 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 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 67 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3660 r_free = 0.3660 target = 0.135510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097248 restraints weight = 25335.990| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.79 r_work: 0.2965 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16986 Z= 0.175 Angle : 0.678 12.765 22982 Z= 0.336 Chirality : 0.042 0.179 2573 Planarity : 0.004 0.058 3017 Dihedral : 9.197 179.594 2423 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 6.46 % Allowed : 29.62 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2068 helix: 2.04 (0.15), residues: 1195 sheet: -0.73 (0.33), residues: 222 loop : -1.55 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 128 HIS 0.006 0.001 HIS B1029 PHE 0.015 0.002 PHE B 886 TYR 0.022 0.002 TYR B 891 ARG 0.007 0.001 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 1004) hydrogen bonds : angle 4.69687 ( 2937) covalent geometry : bond 0.00399 (16986) covalent geometry : angle 0.67827 (22982) *********************** 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 492 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 377 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9092 (ttp) cc_final: 0.8844 (ttm) REVERT: A 792 ARG cc_start: 0.9065 (mtm110) cc_final: 0.8855 (mtm110) REVERT: A 803 GLU cc_start: 0.8460 (tp30) cc_final: 0.8248 (tp30) REVERT: A 813 VAL cc_start: 0.8341 (p) cc_final: 0.8062 (m) REVERT: A 925 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8540 (tp30) REVERT: A 940 ASP cc_start: 0.8501 (t0) cc_final: 0.8295 (t0) REVERT: B 115 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 168 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8792 (mt) REVERT: B 193 ASP cc_start: 0.8793 (t0) cc_final: 0.8527 (t0) REVERT: B 227 ASP cc_start: 0.7976 (p0) cc_final: 0.7506 (p0) REVERT: B 796 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: B 803 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: B 847 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 849 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8109 (t0) REVERT: B 876 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 1020 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8094 (pp) REVERT: B 1060 ASP cc_start: 0.8191 (m-30) cc_final: 0.7960 (m-30) REVERT: B 1073 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8725 (tt0) REVERT: B 1083 GLU cc_start: 0.8528 (pp20) cc_final: 0.7865 (tm-30) REVERT: D 54 GLU cc_start: 0.8565 (tp30) cc_final: 0.8350 (tp30) REVERT: D 79 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: D 112 GLN cc_start: 0.5502 (OUTLIER) cc_final: 0.5229 (tp40) REVERT: E 142 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6573 (tmt170) REVERT: E 163 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8284 (mtp-110) REVERT: E 166 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: E 167 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: E 327 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8203 (tpt90) REVERT: E 386 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7863 (t70) REVERT: E 400 ASP cc_start: 0.8685 (p0) cc_final: 0.8479 (p0) REVERT: E 403 ASP cc_start: 0.8816 (m-30) cc_final: 0.8548 (m-30) outliers start: 115 outliers final: 45 residues processed: 449 average time/residue: 1.3445 time to fit residues: 668.6083 Evaluate side-chains 395 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 336 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain B residue 168 LEU 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 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 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 B residue 1073 GLN Chi-restraints excluded: chain B residue 1075 SER 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 130 SER Chi-restraints excluded: chain E residue 142 ARG 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 171 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B1029 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 = 0.3643 r_free = 0.3643 target = 0.134092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095621 restraints weight = 25420.029| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.76 r_work: 0.2952 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16986 Z= 0.197 Angle : 0.673 12.890 22982 Z= 0.333 Chirality : 0.042 0.179 2573 Planarity : 0.004 0.059 3017 Dihedral : 7.910 167.009 2355 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.51 % Favored : 94.25 % Rotamer: Outliers : 6.86 % Allowed : 30.47 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2068 helix: 1.97 (0.15), residues: 1199 sheet: -0.78 (0.33), residues: 222 loop : -1.59 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 128 HIS 0.005 0.001 HIS B1029 PHE 0.019 0.002 PHE A 221 TYR 0.021 0.001 TYR B 891 ARG 0.008 0.001 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 1004) hydrogen bonds : angle 4.55208 ( 2937) covalent geometry : bond 0.00460 (16986) covalent geometry : angle 0.67329 (22982) *********************** 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 496 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 374 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 792 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (ttp-110) REVERT: A 803 GLU cc_start: 0.8452 (tp30) cc_final: 0.8169 (tp30) REVERT: A 813 VAL cc_start: 0.8331 (p) cc_final: 0.8060 (m) REVERT: A 827 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 905 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7687 (ptp90) REVERT: A 925 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8540 (tp30) REVERT: A 940 ASP cc_start: 0.8514 (t0) cc_final: 0.8293 (t0) REVERT: A 948 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8513 (tm) REVERT: B 79 ASP cc_start: 0.8831 (p0) cc_final: 0.8593 (p0) REVERT: B 115 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 192 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: B 193 ASP cc_start: 0.8800 (t0) cc_final: 0.8598 (t0) REVERT: B 219 GLU cc_start: 0.8632 (mp0) cc_final: 0.8314 (mp0) REVERT: B 796 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: B 803 GLU cc_start: 0.8224 (mp0) cc_final: 0.8003 (mp0) REVERT: B 847 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 849 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8160 (t0) REVERT: B 872 GLU cc_start: 0.8578 (pp20) cc_final: 0.8373 (pp20) REVERT: B 876 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 978 ARG cc_start: 0.2805 (OUTLIER) cc_final: 0.0302 (ttt180) REVERT: B 1020 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 1060 ASP cc_start: 0.8209 (m-30) cc_final: 0.7924 (m-30) REVERT: B 1083 GLU cc_start: 0.8581 (pp20) cc_final: 0.7925 (tm-30) REVERT: D 54 GLU cc_start: 0.8596 (tp30) cc_final: 0.8313 (tp30) REVERT: D 60 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9230 (pt) REVERT: D 79 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: D 112 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4952 (tp40) REVERT: E 142 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6735 (tmt170) REVERT: E 163 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8387 (mtp-110) REVERT: E 167 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8139 (OUTLIER) REVERT: E 327 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8231 (tpt90) REVERT: E 386 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (t70) REVERT: E 403 ASP cc_start: 0.8837 (m-30) cc_final: 0.8569 (m-30) REVERT: E 409 ASP cc_start: 0.8592 (p0) cc_final: 0.8380 (p0) REVERT: E 455 GLU cc_start: 0.8762 (tp30) cc_final: 0.8512 (tp30) outliers start: 122 outliers final: 53 residues processed: 444 average time/residue: 1.3433 time to fit residues: 658.7309 Evaluate side-chains 402 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 334 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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 792 ARG 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 B residue 80 LEU Chi-restraints excluded: chain B residue 168 LEU 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 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 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 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 101 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ARG 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 443 LEU 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 169 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 203 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 250 GLN B 258 GLN B 794 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098422 restraints weight = 25398.815| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.79 r_work: 0.2990 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16986 Z= 0.130 Angle : 0.638 11.780 22982 Z= 0.313 Chirality : 0.040 0.186 2573 Planarity : 0.004 0.055 3017 Dihedral : 7.307 156.599 2345 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.61 % Favored : 94.20 % Rotamer: Outliers : 6.58 % Allowed : 30.52 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2068 helix: 2.09 (0.15), residues: 1197 sheet: -0.69 (0.33), residues: 230 loop : -1.52 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 128 HIS 0.002 0.001 HIS D 139 PHE 0.012 0.001 PHE B 242 TYR 0.021 0.001 TYR B 891 ARG 0.009 0.001 ARG E 282 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1004) hydrogen bonds : angle 4.36700 ( 2937) covalent geometry : bond 0.00291 (16986) covalent geometry : angle 0.63767 (22982) *********************** 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 505 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 388 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 792 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8860 (ttp-110) REVERT: A 813 VAL cc_start: 0.8250 (p) cc_final: 0.8004 (m) REVERT: A 827 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 907 LEU cc_start: 0.9036 (tp) cc_final: 0.8826 (tp) REVERT: A 948 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8459 (tm) REVERT: B 19 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 79 ASP cc_start: 0.8823 (p0) cc_final: 0.8573 (p0) REVERT: B 115 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 192 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7789 (mtp85) REVERT: B 193 ASP cc_start: 0.8772 (t0) cc_final: 0.8523 (t0) REVERT: B 219 GLU cc_start: 0.8556 (mp0) cc_final: 0.8333 (mp0) REVERT: B 250 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8476 (pp30) REVERT: B 796 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7517 (mm-30) REVERT: B 803 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: B 847 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: B 849 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 872 GLU cc_start: 0.8630 (pp20) cc_final: 0.8425 (pp20) REVERT: B 876 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 967 MET cc_start: 0.7818 (mtp) cc_final: 0.7589 (mtp) REVERT: B 978 ARG cc_start: 0.2837 (OUTLIER) cc_final: 0.0291 (ttt180) REVERT: B 1020 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 1060 ASP cc_start: 0.8085 (m-30) cc_final: 0.7807 (m-30) REVERT: B 1083 GLU cc_start: 0.8521 (pp20) cc_final: 0.7851 (tm-30) REVERT: C 164 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: D 54 GLU cc_start: 0.8653 (tp30) cc_final: 0.8358 (tp30) REVERT: D 79 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: D 112 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.5131 (tp40) REVERT: E 130 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8197 (p) REVERT: E 163 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8399 (mtp-110) REVERT: E 317 MET cc_start: 0.8857 (mtm) cc_final: 0.8625 (mtm) REVERT: E 327 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8231 (tpt90) REVERT: E 386 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7907 (t70) REVERT: E 421 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8368 (mp) REVERT: E 455 GLU cc_start: 0.8750 (tp30) cc_final: 0.8502 (tp30) outliers start: 117 outliers final: 43 residues processed: 457 average time/residue: 1.5838 time to fit residues: 804.3054 Evaluate side-chains 399 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 792 ARG 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 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 B residue 60 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 803 GLU 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 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 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 79 GLU 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 130 SER Chi-restraints excluded: chain E residue 143 LEU 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 351 LYS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 250 GLN B1029 HIS 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 = 0.3652 r_free = 0.3652 target = 0.134498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095814 restraints weight = 25630.907| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.80 r_work: 0.2954 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16986 Z= 0.195 Angle : 0.672 11.386 22982 Z= 0.329 Chirality : 0.042 0.226 2573 Planarity : 0.004 0.060 3017 Dihedral : 7.069 144.151 2336 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 6.35 % Allowed : 31.98 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 2068 helix: 2.00 (0.15), residues: 1199 sheet: -0.77 (0.33), residues: 228 loop : -1.53 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 PHE 0.013 0.001 PHE A 242 TYR 0.021 0.002 TYR B 891 ARG 0.011 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1004) hydrogen bonds : angle 4.42538 ( 2937) covalent geometry : bond 0.00454 (16986) covalent geometry : angle 0.67179 (22982) *********************** 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 473 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 360 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9100 (ttp) cc_final: 0.8846 (ttm) REVERT: A 272 TYR cc_start: 0.8843 (t80) cc_final: 0.8630 (t80) REVERT: A 792 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8871 (ttp-110) REVERT: A 803 GLU cc_start: 0.8551 (tp30) cc_final: 0.7815 (tp30) REVERT: A 813 VAL cc_start: 0.8257 (p) cc_final: 0.8009 (m) REVERT: A 827 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8363 (tm-30) REVERT: A 905 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7691 (ptp90) REVERT: A 948 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8531 (tm) REVERT: B 19 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 79 ASP cc_start: 0.8853 (p0) cc_final: 0.8604 (p0) REVERT: B 115 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 128 TRP cc_start: 0.8475 (p90) cc_final: 0.8272 (p90) REVERT: B 171 MET cc_start: 0.8184 (ptm) cc_final: 0.7873 (ptp) REVERT: B 193 ASP cc_start: 0.8783 (t0) cc_final: 0.8543 (t0) REVERT: B 247 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8479 (pp20) REVERT: B 796 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 803 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 849 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8081 (t0) REVERT: B 872 GLU cc_start: 0.8649 (pp20) cc_final: 0.8414 (pp20) REVERT: B 876 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 978 ARG cc_start: 0.2541 (OUTLIER) cc_final: 0.0134 (ttt180) REVERT: B 1020 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8155 (pp) REVERT: B 1060 ASP cc_start: 0.8258 (m-30) cc_final: 0.7936 (m-30) REVERT: B 1083 GLU cc_start: 0.8567 (pp20) cc_final: 0.7900 (tm-30) REVERT: D 54 GLU cc_start: 0.8672 (tp30) cc_final: 0.8399 (tp30) REVERT: D 79 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: D 112 GLN cc_start: 0.5725 (OUTLIER) cc_final: 0.5265 (tp40) REVERT: E 28 ARG cc_start: 0.8891 (mtp-110) cc_final: 0.8410 (mtp-110) REVERT: E 167 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: E 327 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8234 (tpt90) REVERT: E 386 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7869 (t70) REVERT: E 421 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8383 (mp) REVERT: E 455 GLU cc_start: 0.8756 (tp30) cc_final: 0.8529 (tp30) outliers start: 113 outliers final: 57 residues processed: 426 average time/residue: 1.3691 time to fit residues: 648.4746 Evaluate side-chains 413 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 342 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN 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 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 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 B residue 53 VAL Chi-restraints excluded: chain B residue 60 LEU 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 803 GLU Chi-restraints excluded: chain B residue 849 ASN Chi-restraints excluded: chain B residue 871 GLU 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 126 ASN 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 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 253 GLN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 287 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 113 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 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 913 GLN ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN C 232 GLN E 119 ASN E 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096327 restraints weight = 25515.509| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.80 r_work: 0.2964 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16986 Z= 0.173 Angle : 0.670 12.834 22982 Z= 0.327 Chirality : 0.042 0.201 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.834 121.406 2331 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 7.03 % Allowed : 30.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2068 helix: 2.01 (0.15), residues: 1197 sheet: -1.00 (0.32), residues: 240 loop : -1.41 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 128 HIS 0.004 0.001 HIS A1045 PHE 0.013 0.001 PHE A 242 TYR 0.020 0.001 TYR A 891 ARG 0.012 0.001 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1004) hydrogen bonds : angle 4.38388 ( 2937) covalent geometry : bond 0.00403 (16986) covalent geometry : angle 0.67025 (22982) *********************** 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 485 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 360 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3388 (mm) REVERT: A 139 MET cc_start: 0.9088 (ttp) cc_final: 0.8823 (ttm) REVERT: A 792 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8878 (ttp-110) REVERT: A 813 VAL cc_start: 0.8216 (p) cc_final: 0.7928 (m) REVERT: A 827 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 858 GLN cc_start: 0.8304 (mp10) cc_final: 0.8101 (mp10) REVERT: A 925 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: A 948 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8539 (tm) REVERT: B 19 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 37 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9066 (m-30) REVERT: B 79 ASP cc_start: 0.8819 (p0) cc_final: 0.8526 (p0) REVERT: B 115 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 192 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7906 (mmm-85) REVERT: B 193 ASP cc_start: 0.8794 (t0) cc_final: 0.8558 (t0) REVERT: B 247 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: B 784 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7853 (pp20) REVERT: B 803 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: B 849 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 872 GLU cc_start: 0.8661 (pp20) cc_final: 0.8421 (pp20) REVERT: B 876 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 967 MET cc_start: 0.7845 (mtp) cc_final: 0.7402 (mtt) REVERT: B 978 ARG cc_start: 0.2474 (OUTLIER) cc_final: 0.0079 (ttt180) REVERT: B 1020 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8133 (pp) REVERT: B 1060 ASP cc_start: 0.8277 (m-30) cc_final: 0.7941 (m-30) REVERT: B 1083 GLU cc_start: 0.8541 (pp20) cc_final: 0.7895 (tm-30) REVERT: D 54 GLU cc_start: 0.8651 (tp30) cc_final: 0.8378 (tp30) REVERT: D 112 GLN cc_start: 0.5742 (OUTLIER) cc_final: 0.5244 (tp40) REVERT: E 1 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.4528 (pmm) REVERT: E 80 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7514 (tp-100) REVERT: E 163 ARG cc_start: 0.8707 (mtp-110) cc_final: 0.8425 (ttm110) REVERT: E 167 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: E 327 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8243 (tpt90) REVERT: E 386 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (t70) REVERT: E 399 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: E 403 ASP cc_start: 0.8754 (m-30) cc_final: 0.8488 (m-30) REVERT: E 421 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8397 (mp) REVERT: E 455 GLU cc_start: 0.8749 (tp30) cc_final: 0.8511 (tp30) outliers start: 125 outliers final: 62 residues processed: 434 average time/residue: 1.6616 time to fit residues: 798.6232 Evaluate side-chains 420 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 792 ARG 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 881 MET Chi-restraints excluded: chain A residue 891 TYR Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain B residue 37 ASP 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 144 LEU 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 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 103 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN 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 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 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 239 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 287 ASP 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 463 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 250 GLN ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3664 r_free = 0.3664 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096833 restraints weight = 25342.891| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.79 r_work: 0.2973 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2008 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= 0.162 Angle : 0.683 12.337 22982 Z= 0.334 Chirality : 0.043 0.366 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.707 116.751 2331 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 6.18 % Allowed : 32.15 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2068 helix: 2.03 (0.15), residues: 1197 sheet: -0.98 (0.32), residues: 242 loop : -1.41 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 128 HIS 0.003 0.001 HIS A1045 PHE 0.013 0.001 PHE A 242 TYR 0.020 0.001 TYR A 891 ARG 0.012 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1004) hydrogen bonds : angle 4.38572 ( 2937) covalent geometry : bond 0.00378 (16986) covalent geometry : angle 0.68336 (22982) *********************** 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 470 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 360 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3591 (mm) REVERT: A 789 GLU cc_start: 0.8772 (tp30) cc_final: 0.8500 (tp30) REVERT: A 792 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8480 (ttp80) REVERT: A 813 VAL cc_start: 0.8204 (p) cc_final: 0.7916 (m) REVERT: A 827 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 858 GLN cc_start: 0.8309 (mp10) cc_final: 0.8072 (mp10) REVERT: A 948 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8540 (tm) REVERT: B 19 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 37 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.9078 (m-30) REVERT: B 79 ASP cc_start: 0.8805 (p0) cc_final: 0.8497 (p0) REVERT: B 115 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7452 (mm-30) REVERT: B 192 ARG cc_start: 0.8305 (mpp80) cc_final: 0.7972 (mtm180) REVERT: B 193 ASP cc_start: 0.8845 (t0) cc_final: 0.8614 (t0) REVERT: B 784 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7858 (pp20) REVERT: B 803 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 806 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8050 (ttm-80) REVERT: B 872 GLU cc_start: 0.8664 (pp20) cc_final: 0.8433 (pp20) REVERT: B 873 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8460 (tpt-90) REVERT: B 876 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8092 (mm-30) REVERT: B 967 MET cc_start: 0.7931 (mtp) cc_final: 0.7556 (mtt) REVERT: B 978 ARG cc_start: 0.2477 (OUTLIER) cc_final: 0.0083 (ttt180) REVERT: B 1020 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8111 (pp) REVERT: B 1060 ASP cc_start: 0.8302 (m-30) cc_final: 0.7970 (m-30) REVERT: B 1083 GLU cc_start: 0.8480 (pp20) cc_final: 0.7803 (tm-30) REVERT: C 164 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: D 54 GLU cc_start: 0.8644 (tp30) cc_final: 0.8409 (tp30) REVERT: D 112 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5212 (tp40) REVERT: E 1 MET cc_start: 0.4881 (OUTLIER) cc_final: 0.4533 (pmm) REVERT: E 80 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7502 (tp-100) REVERT: E 163 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8449 (ttm110) REVERT: E 167 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: E 277 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8685 (m) REVERT: E 327 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8219 (tpt90) REVERT: E 386 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7866 (t70) REVERT: E 399 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: E 403 ASP cc_start: 0.8760 (m-30) cc_final: 0.8459 (m-30) REVERT: E 421 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8338 (mp) REVERT: E 455 GLU cc_start: 0.8727 (tp30) cc_final: 0.8391 (tp30) REVERT: E 461 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8588 (pp) outliers start: 110 outliers final: 61 residues processed: 429 average time/residue: 1.3363 time to fit residues: 634.2627 Evaluate side-chains 417 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 338 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 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 881 MET 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 966 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 37 ASP 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 250 GLN 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 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 126 ASN 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 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 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 194 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 277 SER Chi-restraints excluded: chain E residue 287 ASP 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 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 186 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 181 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 199 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 250 GLN B 901 HIS ** B1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN E 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100393 restraints weight = 25292.285| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.82 r_work: 0.2991 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16986 Z= 0.144 Angle : 0.680 12.046 22982 Z= 0.332 Chirality : 0.042 0.333 2573 Planarity : 0.004 0.061 3017 Dihedral : 6.569 115.782 2331 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 6.13 % Allowed : 32.27 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2068 helix: 2.04 (0.15), residues: 1202 sheet: -1.00 (0.32), residues: 252 loop : -1.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 128 HIS 0.006 0.001 HIS B 249 PHE 0.013 0.001 PHE A 242 TYR 0.019 0.001 TYR A 891 ARG 0.014 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1004) hydrogen bonds : angle 4.33622 ( 2937) covalent geometry : bond 0.00333 (16986) covalent geometry : angle 0.68039 (22982) *********************** 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 462 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 353 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3581 (mm) REVERT: A 139 MET cc_start: 0.9042 (ttp) cc_final: 0.8771 (ttm) REVERT: A 789 GLU cc_start: 0.8753 (tp30) cc_final: 0.8521 (tp30) REVERT: A 792 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8468 (mtm110) REVERT: A 813 VAL cc_start: 0.8190 (p) cc_final: 0.7922 (m) REVERT: A 827 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 858 GLN cc_start: 0.8321 (mp10) cc_final: 0.8069 (mp10) REVERT: A 948 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8545 (tm) REVERT: B 17 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8392 (ttt90) REVERT: B 37 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.9084 (m-30) REVERT: B 79 ASP cc_start: 0.8790 (p0) cc_final: 0.8456 (p0) REVERT: B 115 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 192 ARG cc_start: 0.8287 (mpp80) cc_final: 0.7974 (mtm180) REVERT: B 193 ASP cc_start: 0.8836 (t0) cc_final: 0.8606 (t0) REVERT: B 784 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7837 (pp20) REVERT: B 803 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 806 ARG cc_start: 0.8447 (tmm-80) cc_final: 0.8094 (ttm-80) REVERT: B 872 GLU cc_start: 0.8664 (pp20) cc_final: 0.8428 (pp20) REVERT: B 873 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8437 (tpt-90) REVERT: B 876 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 967 MET cc_start: 0.7922 (mtp) cc_final: 0.7707 (mtp) REVERT: B 978 ARG cc_start: 0.2540 (OUTLIER) cc_final: 0.0067 (ttt180) REVERT: B 1020 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8103 (pp) REVERT: B 1060 ASP cc_start: 0.8277 (m-30) cc_final: 0.7949 (m-30) REVERT: B 1083 GLU cc_start: 0.8478 (pp20) cc_final: 0.7819 (tm-30) REVERT: C 164 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: D 54 GLU cc_start: 0.8711 (tp30) cc_final: 0.8377 (tp30) REVERT: D 112 GLN cc_start: 0.5788 (OUTLIER) cc_final: 0.5152 (tp40) REVERT: E 1 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.4520 (pmm) REVERT: E 28 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8364 (mtp-110) REVERT: E 51 GLU cc_start: 0.8652 (pm20) cc_final: 0.8358 (mp0) REVERT: E 130 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8223 (p) REVERT: E 163 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.8447 (ttm110) REVERT: E 167 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: E 277 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8654 (m) REVERT: E 327 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8216 (tpt90) REVERT: E 352 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: E 376 GLU cc_start: 0.8152 (pm20) cc_final: 0.7951 (pm20) REVERT: E 386 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7858 (t70) REVERT: E 399 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: E 403 ASP cc_start: 0.8751 (m-30) cc_final: 0.8476 (m-30) REVERT: E 421 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8360 (mp) REVERT: E 455 GLU cc_start: 0.8750 (tp30) cc_final: 0.8395 (tp30) REVERT: E 461 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8559 (pp) outliers start: 109 outliers final: 60 residues processed: 420 average time/residue: 1.5592 time to fit residues: 726.8292 Evaluate side-chains 417 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 338 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 881 MET Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 951 LYS 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 37 ASP 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 250 GLN 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 934 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 1075 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASN 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 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 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 1 MET Chi-restraints excluded: chain E residue 48 ILE 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 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 287 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 62 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 9 optimal weight: 0.0020 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4246 ------------------------------------------------------------------------------- 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 250 GLN B 794 ASN B 901 HIS B1073 GLN C 232 GLN E 80 GLN E 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099087 restraints weight = 25479.541| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.75 r_work: 0.2998 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16986 Z= 0.144 Angle : 0.689 11.878 22982 Z= 0.335 Chirality : 0.042 0.323 2573 Planarity : 0.004 0.059 3017 Dihedral : 6.405 114.198 2329 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 5.68 % Allowed : 32.83 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2068 helix: 2.04 (0.15), residues: 1201 sheet: -0.99 (0.32), residues: 252 loop : -1.37 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 128 HIS 0.006 0.001 HIS B 249 PHE 0.013 0.001 PHE A 242 TYR 0.053 0.002 TYR A 891 ARG 0.014 0.001 ARG E 410 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1004) hydrogen bonds : angle 4.35143 ( 2937) covalent geometry : bond 0.00331 (16986) covalent geometry : angle 0.68911 (22982) *********************** 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 464 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 363 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4120 (OUTLIER) cc_final: 0.3581 (mm) REVERT: A 273 GLN cc_start: 0.8692 (tt0) cc_final: 0.8492 (mt0) REVERT: A 789 GLU cc_start: 0.8746 (tp30) cc_final: 0.8516 (tp30) REVERT: A 792 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8484 (mtm110) REVERT: A 803 GLU cc_start: 0.8630 (tp30) cc_final: 0.7812 (tp30) REVERT: A 813 VAL cc_start: 0.8191 (p) cc_final: 0.7922 (m) REVERT: A 827 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 948 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8548 (tm) REVERT: B 17 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8442 (ttt90) REVERT: B 37 ASP cc_start: 0.9426 (OUTLIER) cc_final: 0.9109 (m-30) REVERT: B 79 ASP cc_start: 0.8804 (p0) cc_final: 0.8456 (p0) REVERT: B 115 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 192 ARG cc_start: 0.8291 (mpp80) cc_final: 0.7957 (mtm180) REVERT: B 193 ASP cc_start: 0.8886 (t0) cc_final: 0.8634 (t0) REVERT: B 784 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7799 (pp20) REVERT: B 803 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 806 ARG cc_start: 0.8451 (tmm-80) cc_final: 0.8040 (ttm-80) REVERT: B 872 GLU cc_start: 0.8659 (pp20) cc_final: 0.8401 (pp20) REVERT: B 873 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8329 (tpp80) REVERT: B 876 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 967 MET cc_start: 0.7910 (mtp) cc_final: 0.7681 (mtp) REVERT: B 978 ARG cc_start: 0.2547 (OUTLIER) cc_final: 0.0080 (ttt180) REVERT: B 1020 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8081 (pp) REVERT: B 1056 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7673 (ttm-80) REVERT: B 1060 ASP cc_start: 0.8221 (m-30) cc_final: 0.7851 (m-30) REVERT: B 1083 GLU cc_start: 0.8478 (pp20) cc_final: 0.7830 (tm-30) REVERT: C 164 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: D 54 GLU cc_start: 0.8664 (tp30) cc_final: 0.8344 (tp30) REVERT: D 112 GLN cc_start: 0.5774 (OUTLIER) cc_final: 0.5134 (tp40) REVERT: E 1 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.4449 (pmm) REVERT: E 28 ARG cc_start: 0.8859 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: E 51 GLU cc_start: 0.8659 (pm20) cc_final: 0.8357 (mp0) REVERT: E 73 ASN cc_start: 0.7306 (m-40) cc_final: 0.6939 (t160) REVERT: E 80 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7801 (tp40) REVERT: E 130 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8207 (p) REVERT: E 163 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8455 (ttm110) REVERT: E 167 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: E 220 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7642 (tm-30) REVERT: E 277 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8636 (m) REVERT: E 327 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8218 (tpt90) REVERT: E 352 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: E 376 GLU cc_start: 0.8178 (pm20) cc_final: 0.7950 (pm20) REVERT: E 386 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7836 (t70) REVERT: E 399 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: E 403 ASP cc_start: 0.8769 (m-30) cc_final: 0.8452 (m-30) REVERT: E 455 GLU cc_start: 0.8743 (tp30) cc_final: 0.8385 (tp30) REVERT: E 461 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8531 (pp) outliers start: 101 outliers final: 60 residues processed: 422 average time/residue: 1.6109 time to fit residues: 754.8724 Evaluate side-chains 429 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 350 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 905 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 951 LYS 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 37 ASP 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 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 871 GLU 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 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 126 ASN 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 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 48 ILE 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 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 287 ASP 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 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 180 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 901 HIS C 232 GLN E 80 GLN E 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097419 restraints weight = 25362.539| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.85 r_work: 0.2964 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16986 Z= 0.192 Angle : 0.716 12.195 22982 Z= 0.350 Chirality : 0.044 0.319 2573 Planarity : 0.004 0.061 3017 Dihedral : 6.448 112.409 2329 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 4.78 % Allowed : 34.12 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2068 helix: 1.93 (0.15), residues: 1202 sheet: -0.95 (0.32), residues: 242 loop : -1.39 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 128 HIS 0.005 0.001 HIS A1045 PHE 0.014 0.002 PHE A 242 TYR 0.047 0.002 TYR A 891 ARG 0.011 0.001 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1004) hydrogen bonds : angle 4.43700 ( 2937) covalent geometry : bond 0.00451 (16986) covalent geometry : angle 0.71627 (22982) ********************** 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 430 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3705 (mm) REVERT: A 789 GLU cc_start: 0.8746 (tp30) cc_final: 0.8509 (tp30) REVERT: A 792 ARG cc_start: 0.9044 (mtm110) cc_final: 0.8662 (mtp85) REVERT: A 803 GLU cc_start: 0.8616 (tp30) cc_final: 0.7780 (tp30) REVERT: A 813 VAL cc_start: 0.8215 (p) cc_final: 0.7980 (m) REVERT: A 827 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 858 GLN cc_start: 0.8269 (mp10) cc_final: 0.7820 (mp10) REVERT: A 948 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (tm) REVERT: B 17 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8415 (ttt90) REVERT: B 37 ASP cc_start: 0.9411 (OUTLIER) cc_final: 0.9106 (m-30) REVERT: B 79 ASP cc_start: 0.8802 (p0) cc_final: 0.8481 (p0) REVERT: B 115 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 192 ARG cc_start: 0.8315 (mpp80) cc_final: 0.7987 (mtm180) REVERT: B 193 ASP cc_start: 0.8908 (t0) cc_final: 0.8661 (t0) REVERT: B 784 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7805 (pp20) REVERT: B 803 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 806 ARG cc_start: 0.8519 (tmm-80) cc_final: 0.8105 (ttm-80) REVERT: B 872 GLU cc_start: 0.8668 (pp20) cc_final: 0.8416 (pp20) REVERT: B 873 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8347 (tpp80) REVERT: B 876 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 967 MET cc_start: 0.7937 (mtp) cc_final: 0.7552 (mtt) REVERT: B 1020 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8098 (pp) REVERT: B 1056 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.7829 (ttm-80) REVERT: B 1060 ASP cc_start: 0.8298 (m-30) cc_final: 0.7922 (m-30) REVERT: B 1083 GLU cc_start: 0.8479 (pp20) cc_final: 0.7797 (tm-30) REVERT: C 164 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: D 54 GLU cc_start: 0.8634 (tp30) cc_final: 0.8310 (tp30) REVERT: D 112 GLN cc_start: 0.5798 (OUTLIER) cc_final: 0.5223 (tp40) REVERT: E 1 MET cc_start: 0.4844 (OUTLIER) cc_final: 0.4509 (pmm) REVERT: E 28 ARG cc_start: 0.8900 (mtp-110) cc_final: 0.8531 (mtp-110) REVERT: E 51 GLU cc_start: 0.8651 (pm20) cc_final: 0.8356 (mp0) REVERT: E 73 ASN cc_start: 0.7431 (m-40) cc_final: 0.6750 (t160) REVERT: E 80 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: E 98 ASP cc_start: 0.8269 (t70) cc_final: 0.8057 (t70) REVERT: E 163 ARG cc_start: 0.8731 (mtp-110) cc_final: 0.8451 (ttm110) REVERT: E 167 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: E 277 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (m) REVERT: E 327 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8191 (tpt90) REVERT: E 334 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: E 352 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: E 386 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7818 (t70) REVERT: E 399 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: E 403 ASP cc_start: 0.8786 (m-30) cc_final: 0.8458 (m-30) REVERT: E 415 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7876 (mm110) REVERT: E 455 GLU cc_start: 0.8767 (tp30) cc_final: 0.8410 (tp30) REVERT: E 461 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8522 (pp) outliers start: 85 outliers final: 61 residues processed: 396 average time/residue: 1.7921 time to fit residues: 787.4245 Evaluate side-chains 418 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 340 time to evaluate : 2.531 ------------------------------------------------------------------------------- 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 237 GLU 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 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 37 ASP 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 281 ASP Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 871 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 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 126 ASN 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 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 48 ILE 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 239 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 287 ASP 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 334 GLU 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 71 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 132 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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** C 232 GLN E 80 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 = 0.3678 r_free = 0.3678 target = 0.136788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100483 restraints weight = 25250.295| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.80 r_work: 0.2984 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16986 Z= 0.167 Angle : 0.711 12.020 22982 Z= 0.346 Chirality : 0.045 0.566 2573 Planarity : 0.004 0.065 3017 Dihedral : 6.399 110.179 2329 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.34 % Rotamer: Outliers : 5.12 % Allowed : 34.06 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2068 helix: 1.97 (0.15), residues: 1200 sheet: -0.94 (0.32), residues: 242 loop : -1.36 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 128 HIS 0.005 0.001 HIS B 901 PHE 0.013 0.001 PHE A 242 TYR 0.045 0.002 TYR A 891 ARG 0.015 0.001 ARG E 410 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 1004) hydrogen bonds : angle 4.41272 ( 2937) covalent geometry : bond 0.00392 (16986) covalent geometry : angle 0.71130 (22982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15116.38 seconds wall clock time: 265 minutes 3.55 seconds (15903.55 seconds total)