Starting phenix.real_space_refine on Wed Aug 5 13:24:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.map" model { file = "/net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sq4_55106/08_2026/9sq4_55106.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 Zn 3 6.06 5 S 63 5.16 5 C 6077 2.51 5 N 1636 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9584 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6270 Classifications: {'peptide': 794} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 767} Chain breaks: 5 Chain: "B" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2982 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 349} Chain breaks: 1 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 309 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 1, 'PHE:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' ZN': 1, 'Y70': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8438 SG CYS B 323 59.494 47.572 26.603 1.00185.04 S ATOM 8462 SG CYS B 326 61.402 44.755 25.385 1.00197.05 S ATOM 8974 SG CYS B 391 62.618 48.241 24.176 1.00194.82 S ATOM 8997 SG CYS B 394 59.851 47.975 23.256 1.00212.68 S ATOM 9273 SG CYS C 384 47.108 69.213 11.833 1.00300.36 S ATOM 9289 SG CYS C 387 48.041 69.935 15.180 1.00292.59 S ATOM 9425 SG CYS C 412 52.114 59.784 19.713 1.00213.30 S ATOM 9441 SG CYS C 415 54.897 58.744 21.813 1.00202.69 S Time building chain proxies: 2.03, per 1000 atoms: 0.21 Number of scatterers: 9584 At special positions: 0 Unit cell: (90.136, 93.5161, 126.19, 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) Zn 3 29.99 S 63 16.00 O 1805 8.00 N 1636 7.00 C 6077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 356.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 323 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 391 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 400 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 404 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 384 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 387 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 428 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 432 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 415 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 412 " Number of angles added : 10 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 20 sheets defined 17.9% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.072A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1062 removed outlier: 4.045A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1061 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1090 through 1096 removed outlier: 3.574A pdb=" N SER A1096 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1125 through 1138 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.877A pdb=" N ALA B 196 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.750A pdb=" N LYS B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 207 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.579A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.747A pdb=" N TYR B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.606A pdb=" N ILE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 318 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.578A pdb=" N HIS C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.482A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A1038 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1029 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A1040 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A1027 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.511A pdb=" N GLY A 17 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 45 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.167A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.352A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.640A pdb=" N HIS A 163 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 192 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP A 207 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU A 194 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 205 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER A 196 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASN A 203 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.579A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 317 removed outlier: 3.544A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 365 removed outlier: 4.127A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.496A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.496A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.339A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 870 through 876 removed outlier: 4.281A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 913 through 917 removed outlier: 6.737A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 954 through 961 removed outlier: 4.097A pdb=" N ALA A 956 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 66 removed outlier: 11.303A pdb=" N ALA B 133 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 168 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 155 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.834A pdb=" N GLN B 179 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 170 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS B 181 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 162 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 139 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 164 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR B 137 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS B 166 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 135 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 168 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N ALA B 133 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B 132 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN B 134 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA B 124 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 136 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 122 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR B 138 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 120 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 330 through 333 removed outlier: 6.841A pdb=" N LEU B 321 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 346 through 350 removed outlier: 7.011A pdb=" N ILE B 398 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS B 397 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N CYS B 391 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 388 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG B 373 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLN B 390 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE B 371 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 410 through 411 removed outlier: 3.572A pdb=" N PHE C 410 " --> pdb=" O PHE C 419 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 990 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: 2.19 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1936 1.33 - 1.45: 2265 1.45 - 1.58: 5475 1.58 - 1.70: 0 1.70 - 1.83: 92 Bond restraints: 9768 Sorted by residual: bond pdb=" CA ILE B 81 " pdb=" CB ILE B 81 " ideal model delta sigma weight residual 1.537 1.555 -0.017 1.29e-02 6.01e+03 1.82e+00 bond pdb=" C VAL A 108 " pdb=" O VAL A 108 " ideal model delta sigma weight residual 1.236 1.222 0.014 1.19e-02 7.06e+03 1.44e+00 bond pdb=" C SER B 239 " pdb=" N TRP B 240 " ideal model delta sigma weight residual 1.333 1.361 -0.029 2.74e-02 1.33e+03 1.11e+00 bond pdb=" CA ASP B 117 " pdb=" C ASP B 117 " ideal model delta sigma weight residual 1.522 1.536 -0.013 1.40e-02 5.10e+03 9.23e-01 bond pdb=" C THR A1082 " pdb=" N GLU A1083 " ideal model delta sigma weight residual 1.329 1.340 -0.012 1.21e-02 6.83e+03 9.11e-01 ... (remaining 9763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 12060 1.21 - 2.42: 966 2.42 - 3.63: 165 3.63 - 4.84: 31 4.84 - 6.05: 8 Bond angle restraints: 13230 Sorted by residual: angle pdb=" N VAL A 995 " pdb=" CA VAL A 995 " pdb=" CB VAL A 995 " ideal model delta sigma weight residual 112.08 106.27 5.81 1.68e+00 3.54e-01 1.20e+01 angle pdb=" CA TYR B 221 " pdb=" CB TYR B 221 " pdb=" CG TYR B 221 " ideal model delta sigma weight residual 113.90 119.95 -6.05 1.80e+00 3.09e-01 1.13e+01 angle pdb=" CA TRP A1047 " pdb=" CB TRP A1047 " pdb=" CG TRP A1047 " ideal model delta sigma weight residual 113.60 119.36 -5.76 1.90e+00 2.77e-01 9.18e+00 angle pdb=" CA ARG A 928 " pdb=" CB ARG A 928 " pdb=" CG ARG A 928 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.67e+00 angle pdb=" C PRO A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 120.97 125.02 -4.05 1.48e+00 4.57e-01 7.50e+00 ... (remaining 13225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 5637 20.84 - 41.68: 214 41.68 - 62.52: 39 62.52 - 83.37: 9 83.37 - 104.21: 6 Dihedral angle restraints: 5905 sinusoidal: 2356 harmonic: 3549 Sorted by residual: dihedral pdb=" CA THR B 333 " pdb=" C THR B 333 " pdb=" N LYS B 334 " pdb=" CA LYS B 334 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C12 Y70 B 501 " pdb=" C14 Y70 B 501 " pdb=" C18 Y70 B 501 " pdb=" C17 Y70 B 501 " ideal model delta sinusoidal sigma weight residual 53.50 -50.71 104.21 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" CA LEU A 317 " pdb=" C LEU A 317 " pdb=" N ASP A 318 " pdb=" CA ASP A 318 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 925 0.059 - 0.117: 400 0.117 - 0.176: 130 0.176 - 0.234: 36 0.234 - 0.293: 9 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA ARG A 928 " pdb=" N ARG A 928 " pdb=" C ARG A 928 " pdb=" CB ARG A 928 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA PHE A 799 " pdb=" N PHE A 799 " pdb=" C PHE A 799 " pdb=" CB PHE A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TYR A 84 " pdb=" N TYR A 84 " pdb=" C TYR A 84 " pdb=" CB TYR A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1497 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 223 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 221 " 0.022 2.00e-02 2.50e+03 1.33e-02 3.53e+00 pdb=" CG TYR B 221 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 221 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 221 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 221 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 221 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 221 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 Y70 B 501 " -0.002 2.00e-02 2.50e+03 9.98e-03 3.24e+00 pdb=" C12 Y70 B 501 " -0.027 2.00e-02 2.50e+03 pdb=" C2 Y70 B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C3 Y70 B 501 " -0.010 2.00e-02 2.50e+03 pdb=" C4 Y70 B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 Y70 B 501 " -0.001 2.00e-02 2.50e+03 pdb=" C6 Y70 B 501 " -0.000 2.00e-02 2.50e+03 pdb=" C7 Y70 B 501 " 0.014 2.00e-02 2.50e+03 pdb=" C9 Y70 B 501 " 0.003 2.00e-02 2.50e+03 pdb=" N10 Y70 B 501 " 0.001 2.00e-02 2.50e+03 pdb=" N8 Y70 B 501 " 0.010 2.00e-02 2.50e+03 pdb=" O11 Y70 B 501 " 0.007 2.00e-02 2.50e+03 pdb=" O13 Y70 B 501 " 0.009 2.00e-02 2.50e+03 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2978 2.83 - 3.35: 8608 3.35 - 3.87: 14983 3.87 - 4.38: 17522 4.38 - 4.90: 30580 Nonbonded interactions: 74671 Sorted by model distance: nonbonded pdb=" O CYS B 326 " pdb=" N GLU B 328 " model vdw 2.313 3.120 nonbonded pdb=" OG SER A 196 " pdb=" OE1 GLU A 199 " model vdw 2.424 3.040 nonbonded pdb=" OG1 THR B 332 " pdb=" OE1 GLU B 336 " model vdw 2.430 3.040 nonbonded pdb=" O TRP B 243 " pdb=" OG SER B 246 " model vdw 2.449 3.040 nonbonded pdb=" O GLU A1134 " pdb=" OG1 THR A1137 " model vdw 2.478 3.040 ... (remaining 74666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.170 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.005 0.169 9781 Z= 0.226 Angle : 0.852 31.890 13242 Z= 0.421 Chirality : 0.075 0.293 1500 Planarity : 0.006 0.060 1701 Dihedral : 12.381 104.208 3606 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.67 % Rotamer: Outliers : 0.29 % Allowed : 4.80 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1203 helix: -1.32 (0.32), residues: 174 sheet: -0.78 (0.22), residues: 420 loop : -1.04 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 270 TYR 0.030 0.003 TYR B 221 PHE 0.026 0.003 PHE A1076 TRP 0.016 0.002 TRP A1047 HIS 0.006 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 9768) covalent geometry : angle 0.73832 / 0.41 (13230) SS BOND : bond 0.00575 / 0.30 ( 1) SS BOND : angle 3.18471 / 1.75 ( 2) hydrogen bonds : bond 0.17760 / 12.07 ( 357) hydrogen bonds : angle 7.84358 / 5.17 ( 990) metal coordination : bond 0.08390 / 5.09 ( 12) metal coordination : angle 15.44825 / 8.20 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8606 (t0) cc_final: 0.8297 (t0) REVERT: A 74 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8921 (mtpt) REVERT: A 90 GLU cc_start: 0.7467 (tt0) cc_final: 0.7245 (tp30) REVERT: A 129 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7568 (mmt180) REVERT: A 197 LEU cc_start: 0.8684 (mt) cc_final: 0.8037 (mp) REVERT: A 209 GLN cc_start: 0.7724 (tp40) cc_final: 0.7225 (tm-30) REVERT: A 224 GLU cc_start: 0.8187 (tp30) cc_final: 0.7808 (tp30) REVERT: A 275 ASP cc_start: 0.7823 (t0) cc_final: 0.7576 (t0) REVERT: A 289 GLU cc_start: 0.8421 (tt0) cc_final: 0.8171 (tp30) REVERT: A 290 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8801 (mm-40) REVERT: A 291 MET cc_start: 0.9020 (mmm) cc_final: 0.8790 (mmm) REVERT: A 303 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 339 ASP cc_start: 0.8097 (m-30) cc_final: 0.7494 (p0) REVERT: A 365 VAL cc_start: 0.8371 (t) cc_final: 0.8057 (m) REVERT: A 367 LEU cc_start: 0.8970 (mt) cc_final: 0.8197 (mt) REVERT: A 372 GLN cc_start: 0.8909 (tt0) cc_final: 0.8679 (tt0) REVERT: A 719 GLU cc_start: 0.7805 (pt0) cc_final: 0.6990 (pt0) REVERT: A 844 LYS cc_start: 0.8476 (mttt) cc_final: 0.8089 (mmmt) REVERT: A 866 VAL cc_start: 0.8358 (t) cc_final: 0.8047 (m) REVERT: A 867 LYS cc_start: 0.8992 (mttt) cc_final: 0.8540 (mtpt) REVERT: A 879 LYS cc_start: 0.8528 (mttm) cc_final: 0.8113 (mmmm) REVERT: A 908 ASN cc_start: 0.8075 (t0) cc_final: 0.7469 (t0) REVERT: A 917 LYS cc_start: 0.8725 (tttt) cc_final: 0.8473 (ttmm) REVERT: A 927 MET cc_start: 0.8476 (mmm) cc_final: 0.8227 (mmm) REVERT: A 928 ARG cc_start: 0.8722 (tpt-90) cc_final: 0.7690 (tpt-90) REVERT: A 969 GLU cc_start: 0.7999 (pt0) cc_final: 0.7487 (pt0) REVERT: A 1042 SER cc_start: 0.8880 (m) cc_final: 0.8335 (p) REVERT: A 1099 ASP cc_start: 0.8874 (m-30) cc_final: 0.8591 (t70) REVERT: A 1106 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 1107 GLU cc_start: 0.9249 (tp30) cc_final: 0.9034 (tp30) REVERT: B 65 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 66 GLU cc_start: 0.8368 (tt0) cc_final: 0.8126 (tm-30) REVERT: B 79 GLN cc_start: 0.8399 (tp40) cc_final: 0.7966 (tp-100) REVERT: B 89 MET cc_start: 0.8856 (ptm) cc_final: 0.8404 (ptm) REVERT: B 117 ASP cc_start: 0.7564 (t0) cc_final: 0.7071 (t70) REVERT: B 156 LYS cc_start: 0.7705 (mttt) cc_final: 0.7298 (mttt) REVERT: B 169 GLU cc_start: 0.7927 (tt0) cc_final: 0.7685 (tt0) REVERT: B 181 LYS cc_start: 0.8864 (tttt) cc_final: 0.8164 (tppt) REVERT: B 183 GLN cc_start: 0.8179 (tp40) cc_final: 0.7716 (tp40) REVERT: B 185 LEU cc_start: 0.8898 (mp) cc_final: 0.8526 (mp) REVERT: B 242 ARG cc_start: 0.8420 (mtt90) cc_final: 0.7891 (mtt90) REVERT: B 251 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 255 ASP cc_start: 0.8491 (t70) cc_final: 0.8268 (t70) REVERT: B 259 LYS cc_start: 0.9192 (tttt) cc_final: 0.8909 (tttt) REVERT: B 260 GLN cc_start: 0.8650 (tp40) cc_final: 0.7891 (tp40) REVERT: B 263 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 268 LEU cc_start: 0.8445 (tp) cc_final: 0.7389 (tp) REVERT: B 273 LEU cc_start: 0.8316 (mm) cc_final: 0.8026 (mm) REVERT: B 295 ARG cc_start: 0.9034 (tpp80) cc_final: 0.8759 (tpt-90) REVERT: B 297 GLN cc_start: 0.9128 (tp40) cc_final: 0.8778 (tp-100) REVERT: B 300 LYS cc_start: 0.8768 (mttt) cc_final: 0.8556 (mttt) REVERT: B 306 GLN cc_start: 0.8487 (tt0) cc_final: 0.7979 (tt0) REVERT: B 316 ASN cc_start: 0.8644 (m110) cc_final: 0.8391 (m-40) REVERT: B 324 LYS cc_start: 0.8971 (tttt) cc_final: 0.8541 (tppt) REVERT: B 328 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 334 LYS cc_start: 0.8332 (pttt) cc_final: 0.7599 (mttt) REVERT: B 337 ILE cc_start: 0.7978 (mt) cc_final: 0.7704 (mt) REVERT: B 346 MET cc_start: 0.8854 (ttm) cc_final: 0.8572 (ttm) REVERT: B 355 TYR cc_start: 0.7757 (m-80) cc_final: 0.6808 (m-80) REVERT: B 361 THR cc_start: 0.7604 (p) cc_final: 0.7259 (p) outliers start: 3 outliers final: 2 residues processed: 334 average time/residue: 0.1169 time to fit residues: 51.1557 Evaluate side-chains 271 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 ASN A 993 GLN A 999 HIS A1034 ASN B 103 HIS B 335 ASN B 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093010 restraints weight = 18634.145| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.31 r_work: 0.3106 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9781 Z= 0.158 Angle : 0.640 12.103 13242 Z= 0.327 Chirality : 0.046 0.174 1500 Planarity : 0.004 0.052 1701 Dihedral : 6.315 69.219 1324 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.11 % Allowed : 11.82 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1203 helix: 0.16 (0.38), residues: 180 sheet: -0.29 (0.23), residues: 466 loop : -0.70 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 198 TYR 0.016 0.001 TYR A 42 PHE 0.024 0.002 PHE B 165 TRP 0.015 0.001 TRP A 893 HIS 0.003 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 9768) covalent geometry : angle 0.62222 / 0.33 (13230) SS BOND : bond 0.00743 / 0.39 ( 1) SS BOND : angle 4.03211 / 2.21 ( 2) hydrogen bonds : bond 0.03896 / 2.65 ( 357) hydrogen bonds : angle 5.30564 / 3.51 ( 990) metal coordination : bond 0.01188 / 0.68 ( 12) metal coordination : angle 5.21956 / 2.95 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 299 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.8741 (t0) cc_final: 0.7772 (t0) REVERT: A 74 LYS cc_start: 0.9332 (mtmt) cc_final: 0.8907 (mtmm) REVERT: A 90 GLU cc_start: 0.8073 (tt0) cc_final: 0.7860 (tp30) REVERT: A 125 ASP cc_start: 0.8350 (t0) cc_final: 0.8078 (t0) REVERT: A 127 GLU cc_start: 0.8102 (tp30) cc_final: 0.7739 (tp30) REVERT: A 129 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8120 (mmt180) REVERT: A 162 LEU cc_start: 0.8951 (mp) cc_final: 0.8718 (mm) REVERT: A 201 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7988 (mm-30) REVERT: A 215 GLU cc_start: 0.8740 (tt0) cc_final: 0.8506 (tt0) REVERT: A 224 GLU cc_start: 0.8681 (tp30) cc_final: 0.8316 (tp30) REVERT: A 339 ASP cc_start: 0.8151 (m-30) cc_final: 0.7746 (p0) REVERT: A 365 VAL cc_start: 0.8663 (t) cc_final: 0.8323 (p) REVERT: A 366 ASP cc_start: 0.7242 (t70) cc_final: 0.6969 (t70) REVERT: A 368 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 369 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7648 (mmm-85) REVERT: A 719 GLU cc_start: 0.8490 (pt0) cc_final: 0.8008 (pt0) REVERT: A 844 LYS cc_start: 0.8893 (mttt) cc_final: 0.8625 (mmmt) REVERT: A 866 VAL cc_start: 0.9001 (t) cc_final: 0.8557 (m) REVERT: A 867 LYS cc_start: 0.9177 (mttt) cc_final: 0.8923 (mtpt) REVERT: A 879 LYS cc_start: 0.8926 (mttm) cc_final: 0.8345 (mttm) REVERT: A 900 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7967 (ttm-80) REVERT: A 908 ASN cc_start: 0.8213 (t0) cc_final: 0.7776 (t0) REVERT: A 927 MET cc_start: 0.8894 (mmm) cc_final: 0.8634 (mmm) REVERT: A 1025 GLN cc_start: 0.8141 (tp40) cc_final: 0.7774 (tp40) REVERT: A 1042 SER cc_start: 0.9282 (m) cc_final: 0.8882 (p) REVERT: A 1057 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8492 (mtt90) REVERT: A 1083 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7184 (mm-30) REVERT: A 1099 ASP cc_start: 0.8784 (m-30) cc_final: 0.8558 (t70) REVERT: A 1105 MET cc_start: 0.8812 (mtp) cc_final: 0.8458 (mtp) REVERT: A 1106 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 1107 GLU cc_start: 0.9215 (tp30) cc_final: 0.8755 (tm-30) REVERT: A 1135 GLU cc_start: 0.8544 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 89 MET cc_start: 0.8604 (ptm) cc_final: 0.8305 (ptm) REVERT: B 135 PHE cc_start: 0.8265 (m-10) cc_final: 0.7918 (m-10) REVERT: B 156 LYS cc_start: 0.8389 (mttt) cc_final: 0.8104 (mttt) REVERT: B 181 LYS cc_start: 0.8841 (tttt) cc_final: 0.8380 (tptt) REVERT: B 183 GLN cc_start: 0.8126 (tp40) cc_final: 0.7763 (tp40) REVERT: B 185 LEU cc_start: 0.9057 (mp) cc_final: 0.8805 (mm) REVERT: B 242 ARG cc_start: 0.8745 (mtt90) cc_final: 0.8326 (mtt90) REVERT: B 251 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 259 LYS cc_start: 0.9219 (tttt) cc_final: 0.9009 (tttt) REVERT: B 260 GLN cc_start: 0.8767 (tp40) cc_final: 0.7568 (tm-30) REVERT: B 262 ARG cc_start: 0.8684 (mmt90) cc_final: 0.8402 (mmt90) REVERT: B 263 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7818 (mt-10) REVERT: B 283 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8737 (tpp80) REVERT: B 297 GLN cc_start: 0.8989 (tp40) cc_final: 0.8624 (tp-100) REVERT: B 316 ASN cc_start: 0.8920 (m110) cc_final: 0.8718 (m-40) REVERT: B 324 LYS cc_start: 0.8992 (tttt) cc_final: 0.8674 (tppt) REVERT: B 334 LYS cc_start: 0.8639 (pttt) cc_final: 0.8230 (mttm) REVERT: B 355 TYR cc_start: 0.7962 (m-80) cc_final: 0.7361 (m-80) REVERT: B 361 THR cc_start: 0.7936 (p) cc_final: 0.7673 (p) REVERT: B 362 VAL cc_start: 0.8692 (m) cc_final: 0.8253 (p) REVERT: B 364 LYS cc_start: 0.8489 (mttt) cc_final: 0.8265 (mttt) REVERT: B 423 LEU cc_start: 0.8838 (tt) cc_final: 0.8428 (tp) outliers start: 22 outliers final: 14 residues processed: 310 average time/residue: 0.1176 time to fit residues: 48.0781 Evaluate side-chains 282 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 268 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 ASN A1034 ASN B 73 HIS B 178 GLN B 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092953 restraints weight = 18627.146| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.32 r_work: 0.3110 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9781 Z= 0.129 Angle : 0.595 10.265 13242 Z= 0.303 Chirality : 0.045 0.185 1500 Planarity : 0.004 0.049 1701 Dihedral : 5.154 55.564 1324 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.07 % Allowed : 15.85 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1203 helix: 0.69 (0.40), residues: 181 sheet: 0.09 (0.24), residues: 450 loop : -0.53 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 171 TYR 0.014 0.001 TYR A 91 PHE 0.012 0.001 PHE B 165 TRP 0.012 0.001 TRP B 386 HIS 0.003 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9768) covalent geometry : angle 0.58337 / 0.30 (13230) SS BOND : bond 0.00770 / 0.41 ( 1) SS BOND : angle 3.05445 / 1.69 ( 2) hydrogen bonds : bond 0.03436 / 2.31 ( 357) hydrogen bonds : angle 4.85922 / 3.22 ( 990) metal coordination : bond 0.00710 / 0.46 ( 12) metal coordination : angle 4.12267 / 2.32 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9320 (mtmt) cc_final: 0.8875 (mtmm) REVERT: A 125 ASP cc_start: 0.8320 (t0) cc_final: 0.7893 (t0) REVERT: A 127 GLU cc_start: 0.8202 (tp30) cc_final: 0.7547 (tp30) REVERT: A 129 ARG cc_start: 0.8481 (mmt180) cc_final: 0.8174 (mmt-90) REVERT: A 136 TYR cc_start: 0.8536 (m-80) cc_final: 0.8138 (m-80) REVERT: A 183 GLN cc_start: 0.7450 (tp40) cc_final: 0.7148 (tp40) REVERT: A 201 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 224 GLU cc_start: 0.8647 (tp30) cc_final: 0.8258 (tp30) REVERT: A 286 GLU cc_start: 0.8018 (tp30) cc_final: 0.7566 (tp30) REVERT: A 307 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8254 (tt0) REVERT: A 312 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 339 ASP cc_start: 0.8108 (m-30) cc_final: 0.7721 (p0) REVERT: A 365 VAL cc_start: 0.8733 (t) cc_final: 0.8370 (p) REVERT: A 366 ASP cc_start: 0.7275 (t70) cc_final: 0.6982 (t70) REVERT: A 367 LEU cc_start: 0.8879 (mt) cc_final: 0.8660 (mt) REVERT: A 368 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 369 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7681 (mmm-85) REVERT: A 719 GLU cc_start: 0.8463 (pt0) cc_final: 0.7774 (pt0) REVERT: A 755 SER cc_start: 0.8308 (p) cc_final: 0.7556 (t) REVERT: A 844 LYS cc_start: 0.8885 (mttt) cc_final: 0.8589 (mmtt) REVERT: A 866 VAL cc_start: 0.8929 (t) cc_final: 0.8568 (m) REVERT: A 867 LYS cc_start: 0.9186 (mttt) cc_final: 0.8913 (mtpt) REVERT: A 879 LYS cc_start: 0.8956 (mttm) cc_final: 0.8623 (mttm) REVERT: A 892 GLU cc_start: 0.8430 (tp30) cc_final: 0.8094 (tp30) REVERT: A 900 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7991 (ttm-80) REVERT: A 908 ASN cc_start: 0.8221 (t0) cc_final: 0.7843 (t0) REVERT: A 927 MET cc_start: 0.8819 (mmm) cc_final: 0.8514 (mmm) REVERT: A 941 ASN cc_start: 0.6836 (p0) cc_final: 0.6428 (m-40) REVERT: A 969 GLU cc_start: 0.8286 (pt0) cc_final: 0.7962 (pt0) REVERT: A 988 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7977 (pt0) REVERT: A 1025 GLN cc_start: 0.8199 (tp40) cc_final: 0.7843 (tp40) REVERT: A 1042 SER cc_start: 0.9268 (m) cc_final: 0.8791 (p) REVERT: A 1083 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 1105 MET cc_start: 0.8759 (mtp) cc_final: 0.8550 (mtp) REVERT: A 1106 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 1107 GLU cc_start: 0.9201 (tp30) cc_final: 0.8785 (tm-30) REVERT: A 1135 GLU cc_start: 0.8572 (tt0) cc_final: 0.8317 (tt0) REVERT: B 89 MET cc_start: 0.8671 (ptm) cc_final: 0.8143 (ppp) REVERT: B 127 ASN cc_start: 0.8113 (t0) cc_final: 0.7567 (t0) REVERT: B 146 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 153 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8018 (mm-30) REVERT: B 156 LYS cc_start: 0.8574 (mttt) cc_final: 0.8325 (mttt) REVERT: B 162 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8254 (mmm-85) REVERT: B 181 LYS cc_start: 0.8474 (tttt) cc_final: 0.8017 (tppt) REVERT: B 185 LEU cc_start: 0.9016 (mp) cc_final: 0.8802 (mm) REVERT: B 242 ARG cc_start: 0.8715 (mtt90) cc_final: 0.8273 (mtt90) REVERT: B 249 ASP cc_start: 0.8354 (t0) cc_final: 0.7982 (t0) REVERT: B 251 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8560 (mm-30) REVERT: B 255 ASP cc_start: 0.8556 (t70) cc_final: 0.8341 (t70) REVERT: B 259 LYS cc_start: 0.9192 (tttt) cc_final: 0.8943 (tttt) REVERT: B 260 GLN cc_start: 0.8742 (tp40) cc_final: 0.7755 (tm-30) REVERT: B 262 ARG cc_start: 0.8808 (mmt90) cc_final: 0.8340 (mmt90) REVERT: B 263 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 283 ARG cc_start: 0.9002 (tpp80) cc_final: 0.8668 (tpp80) REVERT: B 297 GLN cc_start: 0.8995 (tp40) cc_final: 0.8597 (tp-100) REVERT: B 324 LYS cc_start: 0.8865 (tttt) cc_final: 0.8587 (tppt) REVERT: B 334 LYS cc_start: 0.8597 (pttt) cc_final: 0.8142 (mttp) REVERT: B 355 TYR cc_start: 0.7917 (m-80) cc_final: 0.7255 (m-80) REVERT: B 361 THR cc_start: 0.7868 (p) cc_final: 0.7650 (p) REVERT: B 362 VAL cc_start: 0.8642 (m) cc_final: 0.8268 (p) REVERT: B 364 LYS cc_start: 0.8578 (mttt) cc_final: 0.8140 (tttt) outliers start: 32 outliers final: 23 residues processed: 302 average time/residue: 0.1186 time to fit residues: 47.3904 Evaluate side-chains 303 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091996 restraints weight = 18775.724| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.33 r_work: 0.3089 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9781 Z= 0.136 Angle : 0.605 10.920 13242 Z= 0.304 Chirality : 0.045 0.209 1500 Planarity : 0.004 0.047 1701 Dihedral : 4.843 58.191 1324 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.27 % Allowed : 16.71 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1203 helix: 0.77 (0.40), residues: 182 sheet: 0.31 (0.24), residues: 446 loop : -0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 947 TYR 0.015 0.001 TYR A 91 PHE 0.024 0.002 PHE B 165 TRP 0.012 0.001 TRP B 380 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9768) covalent geometry : angle 0.59464 / 0.30 (13230) SS BOND : bond 0.00717 / 0.38 ( 1) SS BOND : angle 2.84096 / 1.57 ( 2) hydrogen bonds : bond 0.03243 / 2.17 ( 357) hydrogen bonds : angle 4.67104 / 3.09 ( 990) metal coordination : bond 0.00679 / 0.44 ( 12) metal coordination : angle 3.89234 / 2.24 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8716 (mtmm) REVERT: A 125 ASP cc_start: 0.8335 (t0) cc_final: 0.7889 (t0) REVERT: A 127 GLU cc_start: 0.8300 (tp30) cc_final: 0.7764 (tp30) REVERT: A 136 TYR cc_start: 0.8510 (m-80) cc_final: 0.8124 (m-80) REVERT: A 183 GLN cc_start: 0.7730 (tp40) cc_final: 0.7350 (tp40) REVERT: A 189 HIS cc_start: 0.8576 (m-70) cc_final: 0.8266 (m-70) REVERT: A 201 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 307 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8272 (tt0) REVERT: A 312 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 339 ASP cc_start: 0.8159 (m-30) cc_final: 0.7682 (p0) REVERT: A 365 VAL cc_start: 0.8726 (t) cc_final: 0.8369 (p) REVERT: A 366 ASP cc_start: 0.7316 (t70) cc_final: 0.7080 (t70) REVERT: A 367 LEU cc_start: 0.8910 (mt) cc_final: 0.8691 (mt) REVERT: A 368 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 369 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7673 (mmm-85) REVERT: A 384 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 719 GLU cc_start: 0.8480 (pt0) cc_final: 0.8168 (pt0) REVERT: A 844 LYS cc_start: 0.8889 (mttt) cc_final: 0.8617 (mmtt) REVERT: A 866 VAL cc_start: 0.8986 (t) cc_final: 0.8689 (m) REVERT: A 867 LYS cc_start: 0.9220 (mttt) cc_final: 0.8955 (mtpt) REVERT: A 875 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 879 LYS cc_start: 0.8956 (mttm) cc_final: 0.8651 (mttm) REVERT: A 892 GLU cc_start: 0.8445 (tp30) cc_final: 0.8119 (tp30) REVERT: A 900 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: A 902 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 908 ASN cc_start: 0.8252 (t0) cc_final: 0.7981 (t0) REVERT: A 927 MET cc_start: 0.8772 (mmm) cc_final: 0.8447 (mmm) REVERT: A 941 ASN cc_start: 0.6805 (p0) cc_final: 0.6567 (m-40) REVERT: A 969 GLU cc_start: 0.8354 (pt0) cc_final: 0.8049 (pt0) REVERT: A 988 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8067 (pt0) REVERT: A 1025 GLN cc_start: 0.8229 (tp40) cc_final: 0.7869 (tp40) REVERT: A 1042 SER cc_start: 0.9245 (m) cc_final: 0.8724 (p) REVERT: A 1083 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 1105 MET cc_start: 0.8747 (mtp) cc_final: 0.8301 (mtp) REVERT: A 1106 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 1107 GLU cc_start: 0.9215 (tp30) cc_final: 0.8811 (tm-30) REVERT: A 1130 ILE cc_start: 0.8693 (mm) cc_final: 0.8446 (tp) REVERT: A 1135 GLU cc_start: 0.8630 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 89 MET cc_start: 0.8682 (ptm) cc_final: 0.8128 (ppp) REVERT: B 117 ASP cc_start: 0.7133 (t0) cc_final: 0.6895 (t0) REVERT: B 129 GLN cc_start: 0.8939 (mp10) cc_final: 0.8434 (pm20) REVERT: B 130 GLU cc_start: 0.8490 (mp0) cc_final: 0.7672 (mp0) REVERT: B 134 GLN cc_start: 0.8085 (pm20) cc_final: 0.7821 (pt0) REVERT: B 135 PHE cc_start: 0.8561 (m-10) cc_final: 0.7898 (m-10) REVERT: B 146 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7617 (tm-30) REVERT: B 153 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 162 ARG cc_start: 0.8465 (mmm160) cc_final: 0.8232 (mmm-85) REVERT: B 181 LYS cc_start: 0.8494 (tttt) cc_final: 0.8168 (tppt) REVERT: B 183 GLN cc_start: 0.8064 (tp40) cc_final: 0.7591 (tp40) REVERT: B 185 LEU cc_start: 0.8971 (mp) cc_final: 0.8743 (mm) REVERT: B 242 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8285 (mtt90) REVERT: B 249 ASP cc_start: 0.8397 (t0) cc_final: 0.7977 (t0) REVERT: B 255 ASP cc_start: 0.8611 (t70) cc_final: 0.8388 (t70) REVERT: B 259 LYS cc_start: 0.9209 (tttt) cc_final: 0.8991 (tttt) REVERT: B 260 GLN cc_start: 0.8846 (tp40) cc_final: 0.8268 (tp40) REVERT: B 262 ARG cc_start: 0.8927 (mmt90) cc_final: 0.8418 (mmt90) REVERT: B 283 ARG cc_start: 0.9025 (tpp80) cc_final: 0.8723 (tpp80) REVERT: B 297 GLN cc_start: 0.8992 (tp40) cc_final: 0.8590 (tp-100) REVERT: B 324 LYS cc_start: 0.8940 (tttt) cc_final: 0.8576 (tppt) REVERT: B 334 LYS cc_start: 0.8567 (pttt) cc_final: 0.8106 (mttp) REVERT: B 340 LEU cc_start: 0.9117 (tp) cc_final: 0.8887 (tp) REVERT: B 355 TYR cc_start: 0.7917 (m-80) cc_final: 0.7294 (m-80) REVERT: B 361 THR cc_start: 0.7858 (p) cc_final: 0.7603 (p) REVERT: B 362 VAL cc_start: 0.8654 (m) cc_final: 0.8281 (p) REVERT: B 364 LYS cc_start: 0.8704 (mttt) cc_final: 0.8462 (mttt) REVERT: B 377 GLU cc_start: 0.7812 (tp30) cc_final: 0.7564 (tp30) outliers start: 34 outliers final: 26 residues processed: 309 average time/residue: 0.1049 time to fit residues: 42.7543 Evaluate side-chains 301 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1140 HIS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A1034 ASN A1055 GLN B 73 HIS ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 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 = 0.3575 r_free = 0.3575 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091049 restraints weight = 18341.882| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.13 r_work: 0.3086 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9781 Z= 0.278 Angle : 0.717 11.170 13242 Z= 0.364 Chirality : 0.047 0.197 1500 Planarity : 0.004 0.050 1701 Dihedral : 5.291 55.797 1323 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.42 % Allowed : 17.20 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1203 helix: 0.60 (0.39), residues: 183 sheet: -0.04 (0.23), residues: 480 loop : -0.44 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 947 TYR 0.017 0.002 TYR A 91 PHE 0.027 0.002 PHE B 165 TRP 0.018 0.002 TRP B 380 HIS 0.007 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 ( 9768) covalent geometry : angle 0.70044 / 0.36 (13230) SS BOND : bond 0.00937 / 0.49 ( 1) SS BOND : angle 3.27822 / 1.81 ( 2) hydrogen bonds : bond 0.04112 / 2.77 ( 357) hydrogen bonds : angle 5.08819 / 3.40 ( 990) metal coordination : bond 0.01224 / 0.87 ( 12) metal coordination : angle 5.47174 / 3.12 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6092 (mmp) cc_final: 0.5786 (mmt) REVERT: A 90 GLU cc_start: 0.7889 (tp30) cc_final: 0.7548 (tm-30) REVERT: A 125 ASP cc_start: 0.8403 (t0) cc_final: 0.8058 (t0) REVERT: A 127 GLU cc_start: 0.8410 (tp30) cc_final: 0.7949 (tp30) REVERT: A 166 ASP cc_start: 0.8464 (t0) cc_final: 0.7906 (p0) REVERT: A 201 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7954 (tp30) REVERT: A 290 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8538 (mm-40) REVERT: A 339 ASP cc_start: 0.8092 (m-30) cc_final: 0.7696 (p0) REVERT: A 365 VAL cc_start: 0.8816 (t) cc_final: 0.8479 (p) REVERT: A 369 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: A 719 GLU cc_start: 0.8419 (pt0) cc_final: 0.8197 (pt0) REVERT: A 802 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8975 (mt) REVERT: A 844 LYS cc_start: 0.9007 (mttt) cc_final: 0.8771 (mmtt) REVERT: A 866 VAL cc_start: 0.8970 (t) cc_final: 0.8704 (m) REVERT: A 867 LYS cc_start: 0.9190 (mttt) cc_final: 0.8932 (mtpt) REVERT: A 875 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 879 LYS cc_start: 0.8868 (mttm) cc_final: 0.8627 (mttm) REVERT: A 889 ARG cc_start: 0.8808 (ttm170) cc_final: 0.8299 (ttm-80) REVERT: A 908 ASN cc_start: 0.8242 (t0) cc_final: 0.7958 (t0) REVERT: A 939 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8118 (mp0) REVERT: A 1061 VAL cc_start: 0.9214 (t) cc_final: 0.8921 (m) REVERT: A 1062 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 1081 LYS cc_start: 0.7938 (pttt) cc_final: 0.7658 (pttt) REVERT: A 1083 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7462 (mp0) REVERT: A 1086 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 1102 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: A 1106 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 1107 GLU cc_start: 0.9131 (tp30) cc_final: 0.8808 (tm-30) REVERT: A 1108 VAL cc_start: 0.9612 (t) cc_final: 0.9070 (p) REVERT: A 1135 GLU cc_start: 0.8606 (tt0) cc_final: 0.7973 (tm-30) REVERT: B 89 MET cc_start: 0.8656 (ptm) cc_final: 0.8393 (ptm) REVERT: B 127 ASN cc_start: 0.8164 (t0) cc_final: 0.6813 (t0) REVERT: B 134 GLN cc_start: 0.8280 (pm20) cc_final: 0.8021 (pm20) REVERT: B 162 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8107 (mmm-85) REVERT: B 242 ARG cc_start: 0.8781 (mtt90) cc_final: 0.8454 (mtt90) REVERT: B 249 ASP cc_start: 0.8587 (t0) cc_final: 0.8198 (t0) REVERT: B 260 GLN cc_start: 0.8876 (tp40) cc_final: 0.7653 (tm-30) REVERT: B 262 ARG cc_start: 0.8834 (mmt90) cc_final: 0.8447 (mmt90) REVERT: B 263 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 283 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8659 (tpp80) REVERT: B 297 GLN cc_start: 0.8974 (tp40) cc_final: 0.8542 (tp-100) REVERT: B 306 GLN cc_start: 0.8410 (tt0) cc_final: 0.7991 (tt0) REVERT: B 324 LYS cc_start: 0.8983 (tttt) cc_final: 0.8736 (ttmm) REVERT: B 334 LYS cc_start: 0.8612 (pttt) cc_final: 0.8196 (mttm) REVERT: B 340 LEU cc_start: 0.9174 (tp) cc_final: 0.8886 (tp) REVERT: B 355 TYR cc_start: 0.7876 (m-80) cc_final: 0.7191 (m-80) REVERT: B 361 THR cc_start: 0.7804 (p) cc_final: 0.7527 (p) REVERT: B 362 VAL cc_start: 0.8804 (m) cc_final: 0.8438 (p) REVERT: B 364 LYS cc_start: 0.8822 (mttt) cc_final: 0.8621 (mttt) outliers start: 46 outliers final: 28 residues processed: 305 average time/residue: 0.0999 time to fit residues: 40.0558 Evaluate side-chains 312 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 59 optimal weight: 0.9980 chunk 100 optimal weight: 0.0070 chunk 3 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A1015 GLN B 73 HIS B 95 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 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 = 0.3570 r_free = 0.3570 target = 0.113227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094353 restraints weight = 18432.556| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.34 r_work: 0.3067 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9781 Z= 0.136 Angle : 0.669 11.719 13242 Z= 0.334 Chirality : 0.045 0.194 1500 Planarity : 0.004 0.042 1701 Dihedral : 4.924 55.408 1323 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.13 % Allowed : 19.31 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.25), residues: 1203 helix: 1.06 (0.42), residues: 176 sheet: 0.24 (0.24), residues: 458 loop : -0.46 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 947 TYR 0.014 0.001 TYR A 91 PHE 0.017 0.001 PHE B 381 TRP 0.016 0.001 TRP A 893 HIS 0.006 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9768) covalent geometry : angle 0.65638 / 0.33 (13230) SS BOND : bond 0.00714 / 0.38 ( 1) SS BOND : angle 2.75530 / 1.52 ( 2) hydrogen bonds : bond 0.03322 / 2.24 ( 357) hydrogen bonds : angle 4.80847 / 3.19 ( 990) metal coordination : bond 0.00646 / 0.47 ( 12) metal coordination : angle 4.62257 / 2.70 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8404 (t0) cc_final: 0.7924 (t0) REVERT: A 127 GLU cc_start: 0.8372 (tp30) cc_final: 0.7736 (tp30) REVERT: A 129 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8094 (mmt180) REVERT: A 136 TYR cc_start: 0.8532 (m-80) cc_final: 0.8229 (m-80) REVERT: A 166 ASP cc_start: 0.8473 (t0) cc_final: 0.7830 (p0) REVERT: A 201 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7996 (tp30) REVERT: A 275 ASP cc_start: 0.8032 (t0) cc_final: 0.7815 (t0) REVERT: A 290 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8649 (mm-40) REVERT: A 299 ASP cc_start: 0.8523 (p0) cc_final: 0.8268 (p0) REVERT: A 307 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8253 (tt0) REVERT: A 339 ASP cc_start: 0.8059 (m-30) cc_final: 0.7616 (p0) REVERT: A 365 VAL cc_start: 0.8699 (t) cc_final: 0.8326 (p) REVERT: A 369 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7782 (mmm-85) REVERT: A 719 GLU cc_start: 0.8525 (pt0) cc_final: 0.8194 (pt0) REVERT: A 720 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.8006 (p) REVERT: A 800 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 844 LYS cc_start: 0.8957 (mttt) cc_final: 0.8661 (mmtt) REVERT: A 889 ARG cc_start: 0.8683 (ttm170) cc_final: 0.8208 (ttm-80) REVERT: A 908 ASN cc_start: 0.8281 (t0) cc_final: 0.7984 (t0) REVERT: A 935 TYR cc_start: 0.8416 (t80) cc_final: 0.8154 (t80) REVERT: A 988 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8354 (pt0) REVERT: A 989 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8336 (mtt-85) REVERT: A 1042 SER cc_start: 0.9160 (m) cc_final: 0.8626 (p) REVERT: A 1045 GLU cc_start: 0.8234 (tt0) cc_final: 0.7854 (tp30) REVERT: A 1062 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 1083 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7330 (mp0) REVERT: A 1102 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7974 (mtp-110) REVERT: A 1105 MET cc_start: 0.8725 (mtp) cc_final: 0.8518 (mtp) REVERT: A 1106 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 1107 GLU cc_start: 0.9183 (tp30) cc_final: 0.8790 (tm-30) REVERT: A 1108 VAL cc_start: 0.9538 (t) cc_final: 0.9007 (p) REVERT: A 1135 GLU cc_start: 0.8661 (tt0) cc_final: 0.7993 (tm-30) REVERT: B 89 MET cc_start: 0.8816 (ptm) cc_final: 0.8612 (ptm) REVERT: B 99 LEU cc_start: 0.8639 (mt) cc_final: 0.8365 (mp) REVERT: B 100 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7863 (tp-100) REVERT: B 127 ASN cc_start: 0.8068 (t0) cc_final: 0.7416 (t0) REVERT: B 156 LYS cc_start: 0.8808 (mttt) cc_final: 0.8254 (mtpt) REVERT: B 181 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7377 (tptp) REVERT: B 183 GLN cc_start: 0.8057 (tp40) cc_final: 0.7590 (tp40) REVERT: B 242 ARG cc_start: 0.8767 (mtt90) cc_final: 0.8356 (mtt90) REVERT: B 249 ASP cc_start: 0.8426 (t0) cc_final: 0.7962 (t0) REVERT: B 260 GLN cc_start: 0.8893 (tp40) cc_final: 0.8329 (tp40) REVERT: B 262 ARG cc_start: 0.8949 (mmt90) cc_final: 0.8541 (mmt90) REVERT: B 283 ARG cc_start: 0.8999 (tpp80) cc_final: 0.8716 (tpp80) REVERT: B 297 GLN cc_start: 0.9003 (tp40) cc_final: 0.8573 (tp-100) REVERT: B 307 ARG cc_start: 0.9096 (ttm-80) cc_final: 0.8837 (ttm170) REVERT: B 324 LYS cc_start: 0.8842 (tttt) cc_final: 0.8471 (ttmm) REVERT: B 334 LYS cc_start: 0.8508 (pttt) cc_final: 0.8098 (mttm) REVERT: B 355 TYR cc_start: 0.7962 (m-80) cc_final: 0.7293 (m-80) REVERT: B 361 THR cc_start: 0.7809 (p) cc_final: 0.7499 (p) REVERT: B 362 VAL cc_start: 0.8727 (m) cc_final: 0.8362 (p) REVERT: B 364 LYS cc_start: 0.8773 (mttt) cc_final: 0.8330 (pttt) outliers start: 43 outliers final: 26 residues processed: 303 average time/residue: 0.0991 time to fit residues: 39.4095 Evaluate side-chains 294 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 709 LYS Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 26 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 290 GLN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 79 GLN B 173 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 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 = 0.3594 r_free = 0.3594 target = 0.113537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094563 restraints weight = 18143.460| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.24 r_work: 0.3086 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9781 Z= 0.239 Angle : 0.741 11.757 13242 Z= 0.372 Chirality : 0.047 0.191 1500 Planarity : 0.004 0.044 1701 Dihedral : 5.254 54.422 1323 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.32 % Allowed : 20.27 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1203 helix: 0.96 (0.41), residues: 182 sheet: 0.00 (0.24), residues: 483 loop : -0.38 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 145 TYR 0.016 0.001 TYR A 42 PHE 0.038 0.002 PHE A1076 TRP 0.017 0.002 TRP A 893 HIS 0.006 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 ( 9768) covalent geometry : angle 0.72057 / 0.37 (13230) SS BOND : bond 0.00876 / 0.46 ( 1) SS BOND : angle 2.95998 / 1.63 ( 2) hydrogen bonds : bond 0.03817 / 2.59 ( 357) hydrogen bonds : angle 4.91041 / 3.27 ( 990) metal coordination : bond 0.01114 / 0.76 ( 12) metal coordination : angle 6.13096 / 3.63 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8042 (tp30) cc_final: 0.7664 (tm-30) REVERT: A 125 ASP cc_start: 0.8420 (t0) cc_final: 0.8013 (t0) REVERT: A 127 GLU cc_start: 0.8410 (tp30) cc_final: 0.7790 (tp30) REVERT: A 129 ARG cc_start: 0.8640 (mmt180) cc_final: 0.8065 (mmt180) REVERT: A 136 TYR cc_start: 0.8548 (m-80) cc_final: 0.8251 (m-80) REVERT: A 151 GLU cc_start: 0.8940 (mp0) cc_final: 0.8726 (mp0) REVERT: A 166 ASP cc_start: 0.8447 (t0) cc_final: 0.7695 (p0) REVERT: A 199 GLU cc_start: 0.8732 (mp0) cc_final: 0.8459 (mp0) REVERT: A 201 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7999 (tp30) REVERT: A 275 ASP cc_start: 0.8118 (t0) cc_final: 0.7846 (t0) REVERT: A 290 GLN cc_start: 0.8958 (mm110) cc_final: 0.8637 (mm-40) REVERT: A 299 ASP cc_start: 0.8526 (p0) cc_final: 0.8289 (p0) REVERT: A 339 ASP cc_start: 0.8076 (m-30) cc_final: 0.7599 (p0) REVERT: A 365 VAL cc_start: 0.8774 (t) cc_final: 0.8427 (p) REVERT: A 366 ASP cc_start: 0.7693 (t0) cc_final: 0.7376 (t0) REVERT: A 369 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: A 719 GLU cc_start: 0.8484 (pt0) cc_final: 0.8241 (pt0) REVERT: A 720 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 800 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 844 LYS cc_start: 0.9011 (mttt) cc_final: 0.8780 (mmtt) REVERT: A 879 LYS cc_start: 0.8901 (mttm) cc_final: 0.8647 (mttm) REVERT: A 889 ARG cc_start: 0.8737 (ttm170) cc_final: 0.8322 (ttm-80) REVERT: A 900 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7641 (ttp80) REVERT: A 908 ASN cc_start: 0.8250 (t0) cc_final: 0.7958 (t0) REVERT: A 927 MET cc_start: 0.8625 (mmm) cc_final: 0.8413 (mmm) REVERT: A 988 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8375 (pt0) REVERT: A 1083 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7487 (mp0) REVERT: A 1102 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8035 (mtp-110) REVERT: A 1104 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8727 (mmpt) REVERT: A 1106 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 1107 GLU cc_start: 0.9147 (tp30) cc_final: 0.8746 (tm-30) REVERT: A 1108 VAL cc_start: 0.9563 (t) cc_final: 0.8944 (p) REVERT: A 1135 GLU cc_start: 0.8615 (tt0) cc_final: 0.8034 (tm-30) REVERT: B 89 MET cc_start: 0.8814 (ptm) cc_final: 0.8566 (ptm) REVERT: B 99 LEU cc_start: 0.8701 (mt) cc_final: 0.8408 (mp) REVERT: B 100 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7990 (tp-100) REVERT: B 127 ASN cc_start: 0.8172 (t0) cc_final: 0.7961 (t0) REVERT: B 156 LYS cc_start: 0.8878 (mttt) cc_final: 0.8303 (mtpt) REVERT: B 162 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.8132 (mmm160) REVERT: B 181 LYS cc_start: 0.8189 (tptt) cc_final: 0.7960 (tppt) REVERT: B 183 GLN cc_start: 0.7591 (tp40) cc_final: 0.7012 (tp40) REVERT: B 249 ASP cc_start: 0.8607 (t0) cc_final: 0.8168 (t0) REVERT: B 260 GLN cc_start: 0.8884 (tp40) cc_final: 0.8305 (tp40) REVERT: B 262 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8582 (mmt90) REVERT: B 297 GLN cc_start: 0.9040 (tp40) cc_final: 0.8582 (tp-100) REVERT: B 324 LYS cc_start: 0.8962 (tttt) cc_final: 0.8606 (ttmm) REVERT: B 334 LYS cc_start: 0.8573 (pttt) cc_final: 0.8201 (mttm) REVERT: B 340 LEU cc_start: 0.9185 (tp) cc_final: 0.8874 (tp) REVERT: B 355 TYR cc_start: 0.7932 (m-80) cc_final: 0.7295 (m-80) REVERT: B 361 THR cc_start: 0.7807 (p) cc_final: 0.7535 (p) REVERT: B 362 VAL cc_start: 0.8771 (m) cc_final: 0.8404 (p) REVERT: B 364 LYS cc_start: 0.8791 (mttt) cc_final: 0.8418 (ttpt) REVERT: B 386 TRP cc_start: 0.8578 (p-90) cc_final: 0.7827 (p-90) outliers start: 45 outliers final: 34 residues processed: 308 average time/residue: 0.0928 time to fit residues: 37.8360 Evaluate side-chains 300 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 91 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 290 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.112261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093238 restraints weight = 18334.568| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.32 r_work: 0.3059 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9781 Z= 0.159 Angle : 0.727 12.470 13242 Z= 0.365 Chirality : 0.046 0.158 1500 Planarity : 0.004 0.039 1701 Dihedral : 5.058 54.035 1323 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 22.48 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1203 helix: 1.07 (0.41), residues: 182 sheet: 0.16 (0.25), residues: 462 loop : -0.47 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 283 TYR 0.014 0.001 TYR A 42 PHE 0.028 0.002 PHE B 165 TRP 0.016 0.001 TRP A 893 HIS 0.005 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9768) covalent geometry : angle 0.71509 / 0.36 (13230) SS BOND : bond 0.00733 / 0.39 ( 1) SS BOND : angle 2.73942 / 1.51 ( 2) hydrogen bonds : bond 0.03389 / 2.29 ( 357) hydrogen bonds : angle 4.73996 / 3.15 ( 990) metal coordination : bond 0.00752 / 0.55 ( 12) metal coordination : angle 4.67041 / 2.74 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8094 (tp30) cc_final: 0.7562 (tm-30) REVERT: A 125 ASP cc_start: 0.8401 (t0) cc_final: 0.7934 (t0) REVERT: A 127 GLU cc_start: 0.8364 (tp30) cc_final: 0.7751 (tp30) REVERT: A 129 ARG cc_start: 0.8653 (mmt180) cc_final: 0.8018 (mmt180) REVERT: A 136 TYR cc_start: 0.8513 (m-80) cc_final: 0.8206 (m-80) REVERT: A 151 GLU cc_start: 0.8913 (mp0) cc_final: 0.8685 (mp0) REVERT: A 166 ASP cc_start: 0.8465 (t0) cc_final: 0.7634 (p0) REVERT: A 199 GLU cc_start: 0.8729 (mp0) cc_final: 0.8478 (mp0) REVERT: A 275 ASP cc_start: 0.8134 (t0) cc_final: 0.7835 (t0) REVERT: A 290 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8674 (mm-40) REVERT: A 299 ASP cc_start: 0.8536 (p0) cc_final: 0.8309 (p0) REVERT: A 339 ASP cc_start: 0.8100 (m-30) cc_final: 0.7575 (p0) REVERT: A 365 VAL cc_start: 0.8720 (t) cc_final: 0.8346 (p) REVERT: A 366 ASP cc_start: 0.7543 (t0) cc_final: 0.7256 (t0) REVERT: A 369 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7714 (mmm-85) REVERT: A 719 GLU cc_start: 0.8542 (pt0) cc_final: 0.8134 (pt0) REVERT: A 720 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 800 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 844 LYS cc_start: 0.8972 (mttt) cc_final: 0.8720 (mmtt) REVERT: A 879 LYS cc_start: 0.8840 (mttm) cc_final: 0.8445 (mttm) REVERT: A 889 ARG cc_start: 0.8667 (ttm170) cc_final: 0.8270 (ttm-80) REVERT: A 900 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7437 (mtp-110) REVERT: A 908 ASN cc_start: 0.8253 (t0) cc_final: 0.7967 (t0) REVERT: A 980 ASP cc_start: 0.8623 (t0) cc_final: 0.8269 (t0) REVERT: A 988 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8386 (pt0) REVERT: A 1053 ASP cc_start: 0.8885 (t0) cc_final: 0.8438 (t0) REVERT: A 1076 PHE cc_start: 0.8176 (t80) cc_final: 0.7876 (t80) REVERT: A 1083 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7283 (mp0) REVERT: A 1102 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (mtp-110) REVERT: A 1104 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8669 (mmpt) REVERT: A 1106 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 1107 GLU cc_start: 0.9194 (tp30) cc_final: 0.8767 (tm-30) REVERT: A 1108 VAL cc_start: 0.9555 (t) cc_final: 0.8933 (p) REVERT: A 1135 GLU cc_start: 0.8689 (tt0) cc_final: 0.8054 (tm-30) REVERT: B 79 GLN cc_start: 0.7447 (tp-100) cc_final: 0.6901 (tp-100) REVERT: B 89 MET cc_start: 0.8882 (ptm) cc_final: 0.8653 (ptm) REVERT: B 99 LEU cc_start: 0.8671 (mt) cc_final: 0.8404 (mp) REVERT: B 100 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7807 (tp-100) REVERT: B 127 ASN cc_start: 0.8131 (t0) cc_final: 0.7771 (t0) REVERT: B 140 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 145 ARG cc_start: 0.7298 (ttp80) cc_final: 0.6968 (ttm170) REVERT: B 156 LYS cc_start: 0.8861 (mttt) cc_final: 0.8185 (mtpp) REVERT: B 162 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.8119 (mmm160) REVERT: B 166 LYS cc_start: 0.8296 (tttt) cc_final: 0.8047 (tttt) REVERT: B 183 GLN cc_start: 0.7534 (tp40) cc_final: 0.6809 (tp40) REVERT: B 249 ASP cc_start: 0.8474 (t0) cc_final: 0.8014 (t0) REVERT: B 260 GLN cc_start: 0.8893 (tp40) cc_final: 0.8281 (tp-100) REVERT: B 262 ARG cc_start: 0.8931 (mmt90) cc_final: 0.8545 (mmt90) REVERT: B 297 GLN cc_start: 0.9048 (tp40) cc_final: 0.8585 (tp-100) REVERT: B 309 ARG cc_start: 0.9063 (mtp85) cc_final: 0.8768 (mtp-110) REVERT: B 324 LYS cc_start: 0.8860 (tttt) cc_final: 0.8485 (ttmm) REVERT: B 334 LYS cc_start: 0.8595 (pttt) cc_final: 0.8189 (mttp) REVERT: B 355 TYR cc_start: 0.7968 (m-80) cc_final: 0.7312 (m-80) REVERT: B 361 THR cc_start: 0.7846 (p) cc_final: 0.7549 (p) REVERT: B 362 VAL cc_start: 0.8728 (m) cc_final: 0.8375 (p) REVERT: B 364 LYS cc_start: 0.8838 (mttt) cc_final: 0.8636 (mttt) REVERT: B 398 ILE cc_start: 0.9300 (mm) cc_final: 0.8958 (tp) outliers start: 39 outliers final: 29 residues processed: 309 average time/residue: 0.0997 time to fit residues: 40.3664 Evaluate side-chains 301 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 290 GLN B 79 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093168 restraints weight = 18279.833| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.32 r_work: 0.3058 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9781 Z= 0.166 Angle : 0.748 12.534 13242 Z= 0.375 Chirality : 0.046 0.155 1500 Planarity : 0.004 0.039 1701 Dihedral : 5.037 54.334 1323 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.17 % Allowed : 23.73 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1203 helix: 1.07 (0.41), residues: 182 sheet: 0.11 (0.24), residues: 471 loop : -0.49 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 947 TYR 0.014 0.001 TYR A 42 PHE 0.031 0.002 PHE B 165 TRP 0.015 0.001 TRP B 380 HIS 0.007 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 9768) covalent geometry : angle 0.73539 / 0.37 (13230) SS BOND : bond 0.00776 / 0.41 ( 1) SS BOND : angle 2.69189 / 1.48 ( 2) hydrogen bonds : bond 0.03384 / 2.27 ( 357) hydrogen bonds : angle 4.73291 / 3.12 ( 990) metal coordination : bond 0.00776 / 0.55 ( 12) metal coordination : angle 4.90030 / 2.91 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8561 (m-30) cc_final: 0.8261 (m-30) REVERT: A 90 GLU cc_start: 0.8021 (tp30) cc_final: 0.7634 (tm-30) REVERT: A 125 ASP cc_start: 0.8395 (t0) cc_final: 0.7921 (t0) REVERT: A 127 GLU cc_start: 0.8367 (tp30) cc_final: 0.7812 (tp30) REVERT: A 129 ARG cc_start: 0.8641 (mmt180) cc_final: 0.8206 (mmt180) REVERT: A 136 TYR cc_start: 0.8514 (m-80) cc_final: 0.8199 (m-80) REVERT: A 151 GLU cc_start: 0.8912 (mp0) cc_final: 0.8674 (mp0) REVERT: A 166 ASP cc_start: 0.8432 (t0) cc_final: 0.7671 (p0) REVERT: A 199 GLU cc_start: 0.8730 (mp0) cc_final: 0.8467 (mp0) REVERT: A 290 GLN cc_start: 0.8950 (mm110) cc_final: 0.8691 (mm-40) REVERT: A 299 ASP cc_start: 0.8536 (p0) cc_final: 0.8308 (p0) REVERT: A 339 ASP cc_start: 0.8106 (m-30) cc_final: 0.7569 (p0) REVERT: A 365 VAL cc_start: 0.8710 (t) cc_final: 0.8342 (p) REVERT: A 366 ASP cc_start: 0.7488 (t0) cc_final: 0.7182 (t0) REVERT: A 719 GLU cc_start: 0.8517 (pt0) cc_final: 0.8143 (pt0) REVERT: A 720 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 800 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 844 LYS cc_start: 0.8975 (mttt) cc_final: 0.8725 (mmtt) REVERT: A 889 ARG cc_start: 0.8642 (ttm170) cc_final: 0.8219 (ttm-80) REVERT: A 900 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7475 (mtp-110) REVERT: A 902 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 908 ASN cc_start: 0.8247 (t0) cc_final: 0.7971 (t0) REVERT: A 935 TYR cc_start: 0.8402 (t80) cc_final: 0.8161 (t80) REVERT: A 980 ASP cc_start: 0.8631 (t0) cc_final: 0.8289 (t0) REVERT: A 988 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8415 (pt0) REVERT: A 994 GLU cc_start: 0.8464 (tt0) cc_final: 0.8223 (tm-30) REVERT: A 1076 PHE cc_start: 0.8130 (t80) cc_final: 0.7826 (t80) REVERT: A 1083 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7316 (mp0) REVERT: A 1102 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8049 (mtp-110) REVERT: A 1104 LYS cc_start: 0.9147 (mmpt) cc_final: 0.8757 (mmpt) REVERT: A 1105 MET cc_start: 0.8696 (mtp) cc_final: 0.8434 (mtp) REVERT: A 1106 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1107 GLU cc_start: 0.9190 (tp30) cc_final: 0.8812 (tm-30) REVERT: A 1108 VAL cc_start: 0.9515 (t) cc_final: 0.9185 (p) REVERT: A 1135 GLU cc_start: 0.8661 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 79 GLN cc_start: 0.7620 (tp40) cc_final: 0.6830 (tp-100) REVERT: B 89 MET cc_start: 0.8868 (ptm) cc_final: 0.8636 (ptm) REVERT: B 99 LEU cc_start: 0.8673 (mt) cc_final: 0.8404 (mp) REVERT: B 100 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7815 (tp-100) REVERT: B 146 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7779 (tp30) REVERT: B 156 LYS cc_start: 0.8883 (mttt) cc_final: 0.8224 (mtpt) REVERT: B 162 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8151 (mmm-85) REVERT: B 166 LYS cc_start: 0.8250 (tttt) cc_final: 0.8006 (tttt) REVERT: B 183 GLN cc_start: 0.7536 (tp40) cc_final: 0.6923 (tp40) REVERT: B 249 ASP cc_start: 0.8491 (t0) cc_final: 0.8011 (t0) REVERT: B 260 GLN cc_start: 0.8877 (tp40) cc_final: 0.8457 (tp40) REVERT: B 297 GLN cc_start: 0.9025 (tp40) cc_final: 0.8583 (tp-100) REVERT: B 307 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8896 (ttm170) REVERT: B 324 LYS cc_start: 0.8821 (tttt) cc_final: 0.8445 (ttmm) REVERT: B 334 LYS cc_start: 0.8600 (pttt) cc_final: 0.8087 (mttm) REVERT: B 355 TYR cc_start: 0.8002 (m-80) cc_final: 0.7355 (m-80) REVERT: B 361 THR cc_start: 0.7887 (p) cc_final: 0.7593 (p) REVERT: B 362 VAL cc_start: 0.8621 (m) cc_final: 0.8253 (p) REVERT: B 364 LYS cc_start: 0.8757 (mttt) cc_final: 0.8329 (ttpt) outliers start: 33 outliers final: 29 residues processed: 300 average time/residue: 0.1027 time to fit residues: 40.1990 Evaluate side-chains 300 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 290 GLN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089288 restraints weight = 18110.445| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.09 r_work: 0.3062 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 9781 Z= 0.339 Angle : 0.855 13.890 13242 Z= 0.432 Chirality : 0.050 0.203 1500 Planarity : 0.005 0.063 1701 Dihedral : 5.642 54.244 1323 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.17 % Allowed : 23.25 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1203 helix: 0.73 (0.40), residues: 183 sheet: -0.03 (0.24), residues: 462 loop : -0.81 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 947 TYR 0.019 0.002 TYR B 349 PHE 0.043 0.003 PHE B 165 TRP 0.023 0.002 TRP A1047 HIS 0.007 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.34 ( 9768) covalent geometry : angle 0.83334 / 0.43 (13230) SS BOND : bond 0.01057 / 0.56 ( 1) SS BOND : angle 3.19792 / 1.77 ( 2) hydrogen bonds : bond 0.04350 / 2.98 ( 357) hydrogen bonds : angle 5.17550 / 3.46 ( 990) metal coordination : bond 0.01649 / 1.22 ( 12) metal coordination : angle 6.91955 / 4.05 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8020 (tp30) cc_final: 0.7768 (tm-30) REVERT: A 125 ASP cc_start: 0.8449 (t0) cc_final: 0.8108 (t0) REVERT: A 127 GLU cc_start: 0.8435 (tp30) cc_final: 0.7885 (tp30) REVERT: A 129 ARG cc_start: 0.8617 (mmt180) cc_final: 0.8163 (mmt180) REVERT: A 151 GLU cc_start: 0.8954 (mp0) cc_final: 0.8710 (mp0) REVERT: A 166 ASP cc_start: 0.8383 (t0) cc_final: 0.7725 (p0) REVERT: A 199 GLU cc_start: 0.8698 (mp0) cc_final: 0.8443 (mp0) REVERT: A 290 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8645 (mm-40) REVERT: A 299 ASP cc_start: 0.8559 (p0) cc_final: 0.8334 (p0) REVERT: A 365 VAL cc_start: 0.8810 (t) cc_final: 0.8505 (p) REVERT: A 719 GLU cc_start: 0.8445 (pt0) cc_final: 0.8159 (pt0) REVERT: A 720 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 800 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 823 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8773 (ptpp) REVERT: A 844 LYS cc_start: 0.9058 (mttt) cc_final: 0.8820 (mmtt) REVERT: A 892 GLU cc_start: 0.8349 (tp30) cc_final: 0.8075 (tm-30) REVERT: A 900 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7692 (ttp80) REVERT: A 902 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 908 ASN cc_start: 0.8199 (t0) cc_final: 0.7924 (t0) REVERT: A 980 ASP cc_start: 0.8645 (t0) cc_final: 0.8330 (t0) REVERT: A 988 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8519 (pt0) REVERT: A 1076 PHE cc_start: 0.8368 (t80) cc_final: 0.8087 (t80) REVERT: A 1083 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7586 (mp0) REVERT: A 1102 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (mtp-110) REVERT: A 1104 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8729 (mmpt) REVERT: A 1106 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1107 GLU cc_start: 0.9206 (tp30) cc_final: 0.8775 (tm-30) REVERT: A 1108 VAL cc_start: 0.9555 (t) cc_final: 0.8935 (p) REVERT: A 1135 GLU cc_start: 0.8655 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 78 CYS cc_start: 0.9071 (t) cc_final: 0.8716 (p) REVERT: B 89 MET cc_start: 0.8800 (ptm) cc_final: 0.8560 (ptm) REVERT: B 99 LEU cc_start: 0.8698 (mt) cc_final: 0.8394 (mp) REVERT: B 100 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7875 (tp-100) REVERT: B 146 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 153 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7958 (mm-30) REVERT: B 156 LYS cc_start: 0.8851 (mttt) cc_final: 0.8310 (mtpt) REVERT: B 183 GLN cc_start: 0.7462 (tp40) cc_final: 0.7134 (tp40) REVERT: B 249 ASP cc_start: 0.8678 (t0) cc_final: 0.8234 (t0) REVERT: B 260 GLN cc_start: 0.8886 (tp40) cc_final: 0.8536 (tp40) REVERT: B 262 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8505 (mmt90) REVERT: B 297 GLN cc_start: 0.9075 (tp40) cc_final: 0.8605 (tp-100) REVERT: B 306 GLN cc_start: 0.8386 (tt0) cc_final: 0.8034 (tt0) REVERT: B 324 LYS cc_start: 0.8995 (tttt) cc_final: 0.8649 (ttmm) REVERT: B 334 LYS cc_start: 0.8632 (pttt) cc_final: 0.8338 (mttm) REVERT: B 340 LEU cc_start: 0.9177 (tp) cc_final: 0.8849 (tp) REVERT: B 361 THR cc_start: 0.7845 (p) cc_final: 0.7597 (p) REVERT: B 362 VAL cc_start: 0.8759 (m) cc_final: 0.8383 (p) REVERT: B 386 TRP cc_start: 0.8597 (p-90) cc_final: 0.7745 (p-90) REVERT: B 392 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8929 (mmmm) outliers start: 33 outliers final: 25 residues processed: 295 average time/residue: 0.1083 time to fit residues: 41.7537 Evaluate side-chains 298 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1075 SER Chi-restraints excluded: chain A residue 1102 ARG Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain C residue 400 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 290 GLN A 372 GLN ** A1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092259 restraints weight = 18161.883| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.14 r_work: 0.3114 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9781 Z= 0.180 Angle : 0.795 12.959 13242 Z= 0.398 Chirality : 0.047 0.180 1500 Planarity : 0.005 0.057 1701 Dihedral : 5.305 58.190 1323 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.36 % Allowed : 23.82 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1203 helix: 0.92 (0.41), residues: 183 sheet: 0.10 (0.25), residues: 447 loop : -0.84 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 947 TYR 0.015 0.001 TYR A 91 PHE 0.079 0.002 PHE B 150 TRP 0.025 0.002 TRP A1047 HIS 0.004 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9768) covalent geometry : angle 0.78196 / 0.40 (13230) SS BOND : bond 0.00798 / 0.42 ( 1) SS BOND : angle 2.88426 / 1.59 ( 2) hydrogen bonds : bond 0.03482 / 2.38 ( 357) hydrogen bonds : angle 4.87340 / 3.25 ( 990) metal coordination : bond 0.00942 / 0.68 ( 12) metal coordination : angle 5.20506 / 3.00 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.97 seconds wall clock time: 32 minutes 13.25 seconds (1933.25 seconds total)