Starting phenix.real_space_refine on Mon Oct 26 15:26:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4t_72497/10_2026/9y4t_72497.map" } resolution = 3.14 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= 1.216 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: 8 Type Number sf(0) Gaussians P 11 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6616 2.51 5 N 1553 2.21 5 O 1736 1.98 5 F 2 1.80 5 H 9568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1152, 18741 Classifications: {'peptide': 1152} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 1120} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1152, 18741 Classifications: {'peptide': 1152} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 1120} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 18829 Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 687 Unusual residues: {' MG': 2, 'AJP': 2, 'ATP': 2, 'CLR': 10, 'CPL': 1, 'D12': 2, 'HEX': 1, 'MYS': 1, 'OCT': 1, 'OLA': 1, 'PLM': 1, 'PTY': 2, 'VX8': 1} Classifications: {'peptide': 2, 'undetermined': 27} Link IDs: {'TRANS': 1, None: 27} Not linked: pdbres="AJP A4001 " pdbres="CLR A4002 " Not linked: pdbres="CLR A4002 " pdbres="CLR A4003 " Not linked: pdbres="CLR A4003 " pdbres="CLR A4004 " Not linked: pdbres="CLR A4004 " pdbres="P5S A4005 " Not linked: pdbres="P5S A4006 " pdbres="CLR A4007 " ... (remaining 22 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 50 residue: pdb=" N MET A 1 " occ=0.88 ... (17 atoms not shown) pdb=" HE3 MET A 1 " occ=0.88 residue: pdb=" N GLN A 2 " occ=0.88 ... (15 atoms not shown) pdb="HE22 GLN A 2 " occ=0.88 residue: pdb=" N ARG A 3 " occ=0.88 ... (22 atoms not shown) pdb="HH22 ARG A 3 " occ=0.88 residue: pdb=" N SER A 4 " occ=0.88 ... (9 atoms not shown) pdb=" HG SER A 4 " occ=0.88 residue: pdb=" N PRO A 5 " occ=0.88 ... (12 atoms not shown) pdb=" HD3 PRO A 5 " occ=0.88 residue: pdb=" N LEU A 6 " occ=0.88 ... (17 atoms not shown) pdb="HD23 LEU A 6 " occ=0.88 residue: pdb=" N GLU A 7 " occ=0.88 ... (13 atoms not shown) pdb=" HG3 GLU A 7 " occ=0.88 residue: pdb=" N LYS A 8 " occ=0.88 ... (20 atoms not shown) pdb=" HZ3 LYS A 8 " occ=0.88 residue: pdb=" N ALA A 9 " occ=0.88 ... (8 atoms not shown) pdb=" HB3 ALA A 9 " occ=0.88 residue: pdb=" N SER A 10 " occ=0.88 ... (9 atoms not shown) pdb=" HG SER A 10 " occ=0.88 residue: pdb=" N VAL A 11 " occ=0.88 ... (14 atoms not shown) pdb="HG23 VAL A 11 " occ=0.88 residue: pdb=" N VAL A 12 " occ=0.88 ... (14 atoms not shown) pdb="HG23 VAL A 12 " occ=0.88 ... (remaining 38 not shown) Time building chain proxies: 5.77, per 1000 atoms: 0.30 Number of scatterers: 19536 At special positions: 0 Unit cell: (76.36, 106.24, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 11 15.00 Mg 2 11.99 F 2 9.00 O 1736 8.00 N 1553 7.00 C 6616 6.00 H 9568 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 739.5 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 68.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.836A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 63 removed outlier: 3.566A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 108 removed outlier: 3.804A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 117 through 165 removed outlier: 4.200A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.815A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 4.173A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 199 through 220 Proline residue: A 205 - end of helix removed outlier: 3.507A pdb=" N ALA A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.882A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 277 through 329 removed outlier: 3.624A pdb=" N GLN A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.574A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.540A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 635 removed outlier: 4.090A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 854 removed outlier: 3.668A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 885 removed outlier: 4.155A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 removed outlier: 3.570A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.636A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 958 removed outlier: 3.718A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 968 through 986 removed outlier: 3.796A pdb=" N ILE A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 Processing helix chain 'A' and resid 1012 through 1035 removed outlier: 4.150A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1018 " --> pdb=" O TYR A1014 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.677A pdb=" N VAL A1024 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1061 Proline residue: A1050 - end of helix Processing helix chain 'A' and resid 1061 through 1067 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.519A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1168 removed outlier: 3.651A pdb=" N VAL A1129 " --> pdb=" O GLY A1125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1259 Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1324 through 1331 removed outlier: 3.591A pdb=" N ILE A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 3.794A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 447 removed outlier: 5.459A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 397 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 479 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.427A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 6.907A pdb=" N GLU A1228 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR A1216 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.700A pdb=" N VAL A1240 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU A1401 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A1242 " --> pdb=" O GLU A1401 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG A1239 " --> pdb=" O GLN A1412 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A1414 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY A1241 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE A1416 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A1243 " --> pdb=" O ILE A1416 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1602 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: 4.44 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9553 1.03 - 1.23: 30 1.23 - 1.42: 4028 1.42 - 1.62: 6066 1.62 - 1.81: 91 Bond restraints: 19768 Sorted by residual: bond pdb=" C17 VX8 A4029 " pdb=" C18 VX8 A4029 " ideal model delta sigma weight residual 1.369 1.586 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C16 VX8 A4029 " pdb=" O5 VX8 A4029 " ideal model delta sigma weight residual 1.368 1.562 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C15 VX8 A4029 " pdb=" C16 VX8 A4029 " ideal model delta sigma weight residual 1.367 1.534 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C17 VX8 A4029 " pdb=" O4 VX8 A4029 " ideal model delta sigma weight residual 1.368 1.229 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C20 VX8 A4029 " pdb=" O4 VX8 A4029 " ideal model delta sigma weight residual 1.370 1.254 0.116 2.00e-02 2.50e+03 3.37e+01 ... (remaining 19763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 35473 4.54 - 9.08: 58 9.08 - 13.63: 6 13.63 - 18.17: 1 18.17 - 22.71: 2 Bond angle restraints: 35540 Sorted by residual: angle pdb=" C14 VX8 A4029 " pdb=" C13 VX8 A4029 " pdb=" C22 VX8 A4029 " ideal model delta sigma weight residual 117.72 140.43 -22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C17 VX8 A4029 " pdb=" O4 VX8 A4029 " pdb=" C20 VX8 A4029 " ideal model delta sigma weight residual 107.00 126.68 -19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" C15 VX8 A4029 " pdb=" C16 VX8 A4029 " pdb=" O5 VX8 A4029 " ideal model delta sigma weight residual 129.02 143.87 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C18 VX8 A4029 " pdb=" C17 VX8 A4029 " pdb=" O4 VX8 A4029 " ideal model delta sigma weight residual 129.56 141.17 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C17 VX8 A4029 " pdb=" C18 VX8 A4029 " pdb=" C19 VX8 A4029 " ideal model delta sigma weight residual 115.95 127.40 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 35535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.74: 9555 30.74 - 61.49: 391 61.49 - 92.23: 37 92.23 - 122.97: 13 122.97 - 153.72: 7 Dihedral angle restraints: 10003 sinusoidal: 5944 harmonic: 4059 Sorted by residual: dihedral pdb=" C12 VX8 A4029 " pdb=" C13 VX8 A4029 " pdb=" C21 VX8 A4029 " pdb=" C22 VX8 A4029 " ideal model delta sinusoidal sigma weight residual 253.58 99.86 153.72 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C17 VX8 A4029 " pdb=" C20 VX8 A4029 " pdb=" O4 VX8 A4029 " pdb=" F1 VX8 A4029 " ideal model delta sinusoidal sigma weight residual 239.99 95.12 144.87 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C16 VX8 A4029 " pdb=" C20 VX8 A4029 " pdb=" O5 VX8 A4029 " pdb=" F1 VX8 A4029 " ideal model delta sinusoidal sigma weight residual 120.10 -99.13 -140.77 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 10000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1568 0.125 - 0.251: 32 0.251 - 0.376: 6 0.376 - 0.501: 0 0.501 - 0.627: 1 Chirality restraints: 1607 Sorted by residual: chirality pdb=" C13 VX8 A4029 " pdb=" C12 VX8 A4029 " pdb=" C14 VX8 A4029 " pdb=" C22 VX8 A4029 " both_signs ideal model delta sigma weight residual True 1.48 0.85 0.63 2.00e-01 2.50e+01 9.82e+00 chirality pdb=" C06 AJP A4018 " pdb=" C05 AJP A4018 " pdb=" C07 AJP A4018 " pdb=" C83 AJP A4018 " both_signs ideal model delta sigma weight residual False 2.54 2.85 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C27 AJP A4001 " pdb=" C26 AJP A4001 " pdb=" C28 AJP A4001 " pdb=" O78 AJP A4001 " both_signs ideal model delta sigma weight residual False -2.44 -2.75 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1604 not shown) Planarity restraints: 2726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1377 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A1378 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1378 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1378 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1274 " 0.011 2.00e-02 2.50e+03 8.25e-03 2.72e+00 pdb=" CG TRP A1274 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A1274 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A1274 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1274 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1274 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1274 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1274 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1274 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1274 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A1274 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A1274 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A1274 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1274 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1274 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A1274 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1057 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C THR A1057 " 0.028 2.00e-02 2.50e+03 pdb=" O THR A1057 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A1058 " -0.009 2.00e-02 2.50e+03 ... (remaining 2723 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 3890 2.31 - 2.88: 43705 2.88 - 3.45: 49523 3.45 - 4.03: 67071 4.03 - 4.60: 104099 Nonbonded interactions: 268288 Sorted by model distance: nonbonded pdb=" HB2 SER A1251 " pdb="MG MG A4028 " model vdw 1.732 1.870 nonbonded pdb=" O3B ATP A4027 " pdb="MG MG A4028 " model vdw 1.859 2.050 nonbonded pdb=" O1A ATP A4025 " pdb="MG MG A4026 " model vdw 1.925 2.050 nonbonded pdb=" HH TYR A1219 " pdb=" HG1 THR A1252 " model vdw 1.942 2.100 nonbonded pdb=" HZ PHE A1232 " pdb=" HZ PHE A1257 " model vdw 1.946 2.100 ... (remaining 268283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.43 max=1.00 mean=0.99 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.007 0.217 10200 Z= 0.311 Angle : 0.870 22.710 13845 Z= 0.415 Chirality : 0.050 0.627 1607 Planarity : 0.004 0.063 1600 Dihedral : 17.180 153.717 4614 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.02 (0.25), residues: 1152 helix: 0.95 (0.20), residues: 731 sheet: -2.18 (0.61), residues: 50 loop : -1.60 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1301 TYR 0.015 0.001 TYR A 385 PHE 0.018 0.002 PHE A 305 TRP 0.027 0.002 TRP A1274 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.31 (10200) covalent geometry : angle 0.87004 / 0.41 (13845) hydrogen bonds : bond 0.15119 / 10.09 ( 545) hydrogen bonds : angle 6.14851 / 4.22 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7963 (pm20) cc_final: 0.7684 (pm20) REVERT: A 44 ASP cc_start: 0.8100 (t0) cc_final: 0.7843 (t0) REVERT: A 59 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7540 (ttm-80) REVERT: A 245 MET cc_start: 0.6653 (mmm) cc_final: 0.6057 (ttp) REVERT: A 256 SER cc_start: 0.7912 (t) cc_final: 0.7633 (p) REVERT: A 348 MET cc_start: 0.8628 (tpp) cc_final: 0.8257 (tpp) REVERT: A 632 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 985 ASP cc_start: 0.8381 (p0) cc_final: 0.8138 (p0) REVERT: A 1341 ASP cc_start: 0.8532 (t0) cc_final: 0.7888 (m-30) REVERT: A 1403 ARG cc_start: 0.7437 (tpt170) cc_final: 0.7159 (tpt170) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2227 time to fit residues: 45.1287 Evaluate side-chains 122 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122704 restraints weight = 69415.712| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.55 r_work: 0.3315 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10200 Z= 0.136 Angle : 0.512 6.230 13845 Z= 0.269 Chirality : 0.036 0.142 1607 Planarity : 0.003 0.052 1600 Dihedral : 13.440 146.769 2402 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.67 (0.26), residues: 1152 helix: 1.65 (0.20), residues: 733 sheet: -2.63 (0.50), residues: 80 loop : -1.44 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.010 0.001 TYR A 28 PHE 0.018 0.001 PHE A1107 TRP 0.018 0.001 TRP A1274 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10200) covalent geometry : angle 0.51239 / 0.27 (13845) hydrogen bonds : bond 0.04679 / 3.11 ( 545) hydrogen bonds : angle 4.30870 / 3.02 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7907 (pm20) cc_final: 0.7649 (pm20) REVERT: A 44 ASP cc_start: 0.7976 (t0) cc_final: 0.7640 (t0) REVERT: A 245 MET cc_start: 0.6887 (mmm) cc_final: 0.6197 (ttp) REVERT: A 256 SER cc_start: 0.7955 (t) cc_final: 0.7632 (p) REVERT: A 632 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 985 ASP cc_start: 0.8075 (p0) cc_final: 0.7823 (p0) REVERT: A 1145 TRP cc_start: 0.7498 (m-10) cc_final: 0.7285 (m-10) REVERT: A 1341 ASP cc_start: 0.8583 (t0) cc_final: 0.7882 (m-30) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2509 time to fit residues: 44.7056 Evaluate side-chains 120 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [37, 66, 92, 26, 55, 9, 76, 79, 27, 58, 91] chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117526 restraints weight = 64737.093| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.44 r_work: 0.3294 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10200 Z= 0.163 Angle : 0.516 6.268 13845 Z= 0.270 Chirality : 0.036 0.137 1607 Planarity : 0.004 0.051 1600 Dihedral : 12.887 145.063 2402 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.20 % Allowed : 6.61 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.89 (0.26), residues: 1152 helix: 1.85 (0.20), residues: 735 sheet: -2.75 (0.53), residues: 69 loop : -1.46 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.008 0.001 TYR A 84 PHE 0.011 0.001 PHE A 508 TRP 0.022 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10200) covalent geometry : angle 0.51561 / 0.27 (13845) hydrogen bonds : bond 0.04670 / 3.12 ( 545) hydrogen bonds : angle 4.13523 / 2.89 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 2 GLN cc_start: 0.7947 (pm20) cc_final: 0.7693 (pm20) REVERT: A 44 ASP cc_start: 0.8009 (t0) cc_final: 0.7666 (t0) REVERT: A 245 MET cc_start: 0.6853 (mmm) cc_final: 0.6200 (ttm) REVERT: A 256 SER cc_start: 0.7959 (t) cc_final: 0.7625 (p) REVERT: A 517 TYR cc_start: 0.8660 (t80) cc_final: 0.8436 (t80) REVERT: A 632 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 985 ASP cc_start: 0.8091 (p0) cc_final: 0.7833 (p0) REVERT: A 1145 TRP cc_start: 0.7508 (m-10) cc_final: 0.7306 (m-10) REVERT: A 1341 ASP cc_start: 0.8565 (t0) cc_final: 0.7871 (m-30) REVERT: A 1429 LYS cc_start: 0.8554 (mmtm) cc_final: 0.7973 (mtpp) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.2418 time to fit residues: 42.7552 Evaluate side-chains 117 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [31, 28, 15, 111, 57, 20, 12, 10, 85, 21, 4] chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119055 restraints weight = 79013.738| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.73 r_work: 0.3279 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.140 Angle : 0.480 6.194 13845 Z= 0.253 Chirality : 0.036 0.138 1607 Planarity : 0.003 0.050 1600 Dihedral : 12.624 145.331 2402 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.39 % Allowed : 7.40 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.06 (0.26), residues: 1152 helix: 1.99 (0.20), residues: 735 sheet: -2.50 (0.56), residues: 65 loop : -1.48 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.005 0.001 TYR A 563 PHE 0.009 0.001 PHE A1107 TRP 0.021 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10200) covalent geometry : angle 0.47957 / 0.25 (13845) hydrogen bonds : bond 0.04259 / 2.83 ( 545) hydrogen bonds : angle 3.99068 / 2.79 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.486 Fit side-chains REVERT: A 44 ASP cc_start: 0.7972 (t0) cc_final: 0.7610 (t0) REVERT: A 245 MET cc_start: 0.6862 (mmm) cc_final: 0.6256 (ttm) REVERT: A 256 SER cc_start: 0.7998 (t) cc_final: 0.7650 (p) REVERT: A 517 TYR cc_start: 0.8639 (t80) cc_final: 0.8348 (t80) REVERT: A 632 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 985 ASP cc_start: 0.8012 (p0) cc_final: 0.7733 (p0) REVERT: A 1145 TRP cc_start: 0.7532 (m-10) cc_final: 0.7326 (m-10) REVERT: A 1305 ASP cc_start: 0.8291 (t0) cc_final: 0.7870 (t70) REVERT: A 1341 ASP cc_start: 0.8663 (t0) cc_final: 0.7913 (m-30) REVERT: A 1348 HIS cc_start: 0.7634 (t-90) cc_final: 0.7400 (t-90) REVERT: A 1429 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8093 (mtpp) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.2263 time to fit residues: 41.2526 Evaluate side-chains 120 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [100, 63, 7, 23, 90, 92, 103, 88, 32, 94, 74] chunk 100 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115747 restraints weight = 69535.273| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.48 r_work: 0.3274 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10200 Z= 0.169 Angle : 0.505 6.259 13845 Z= 0.266 Chirality : 0.036 0.140 1607 Planarity : 0.003 0.050 1600 Dihedral : 12.483 144.658 2402 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.39 % Allowed : 8.19 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.06 (0.26), residues: 1152 helix: 1.98 (0.20), residues: 740 sheet: -2.57 (0.57), residues: 65 loop : -1.50 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.007 0.001 TYR A 563 PHE 0.012 0.001 PHE A1300 TRP 0.027 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10200) covalent geometry : angle 0.50504 / 0.27 (13845) hydrogen bonds : bond 0.04414 / 2.94 ( 545) hydrogen bonds : angle 4.00470 / 2.80 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.528 Fit side-chains REVERT: A 44 ASP cc_start: 0.7987 (t0) cc_final: 0.7647 (t0) REVERT: A 245 MET cc_start: 0.6882 (mmm) cc_final: 0.6275 (ttp) REVERT: A 256 SER cc_start: 0.7984 (t) cc_final: 0.7638 (p) REVERT: A 303 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7642 (mtp180) REVERT: A 517 TYR cc_start: 0.8658 (t80) cc_final: 0.8451 (t80) REVERT: A 632 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 1145 TRP cc_start: 0.7478 (m-10) cc_final: 0.7273 (m-10) REVERT: A 1305 ASP cc_start: 0.8314 (t0) cc_final: 0.7950 (t70) REVERT: A 1341 ASP cc_start: 0.8635 (t0) cc_final: 0.7875 (m-30) REVERT: A 1429 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8235 (mtpp) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 0.2320 time to fit residues: 38.9889 Evaluate side-chains 119 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [76, 19, 37, 99, 16, 2, 75, 33, 67, 104, 74] chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118172 restraints weight = 72619.302| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.75 r_work: 0.3279 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10200 Z= 0.128 Angle : 0.467 6.239 13845 Z= 0.246 Chirality : 0.036 0.136 1607 Planarity : 0.003 0.050 1600 Dihedral : 12.193 145.261 2402 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.39 % Allowed : 8.09 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.23 (0.26), residues: 1152 helix: 2.13 (0.20), residues: 736 sheet: -2.61 (0.62), residues: 55 loop : -1.46 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 248 TYR 0.005 0.001 TYR A 304 PHE 0.009 0.001 PHE A1107 TRP 0.023 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10200) covalent geometry : angle 0.46715 / 0.25 (13845) hydrogen bonds : bond 0.04089 / 2.72 ( 545) hydrogen bonds : angle 3.89531 / 2.72 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.533 Fit side-chains REVERT: A 44 ASP cc_start: 0.7922 (t0) cc_final: 0.7588 (t0) REVERT: A 245 MET cc_start: 0.6875 (mmm) cc_final: 0.6359 (ttm) REVERT: A 256 SER cc_start: 0.7959 (t) cc_final: 0.7614 (p) REVERT: A 517 TYR cc_start: 0.8620 (t80) cc_final: 0.8363 (t80) REVERT: A 632 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 1145 TRP cc_start: 0.7433 (m-10) cc_final: 0.7231 (m-10) REVERT: A 1305 ASP cc_start: 0.8211 (t0) cc_final: 0.7699 (t0) REVERT: A 1341 ASP cc_start: 0.8610 (t0) cc_final: 0.7877 (m-30) REVERT: A 1429 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8244 (mtpp) outliers start: 4 outliers final: 4 residues processed: 125 average time/residue: 0.2250 time to fit residues: 39.9291 Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [51, 2, 72, 98, 60, 93, 15, 79, 94, 49, 64] chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115159 restraints weight = 78312.851| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.04 r_work: 0.3224 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.143 Angle : 0.479 6.285 13845 Z= 0.252 Chirality : 0.036 0.138 1607 Planarity : 0.003 0.050 1600 Dihedral : 12.130 144.986 2402 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.49 % Allowed : 7.80 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.23 (0.26), residues: 1152 helix: 2.12 (0.20), residues: 741 sheet: -2.63 (0.61), residues: 55 loop : -1.49 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1301 TYR 0.006 0.001 TYR A 563 PHE 0.010 0.001 PHE A1300 TRP 0.025 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10200) covalent geometry : angle 0.47918 / 0.25 (13845) hydrogen bonds : bond 0.04146 / 2.76 ( 545) hydrogen bonds : angle 3.89126 / 2.72 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.503 Fit side-chains REVERT: A 44 ASP cc_start: 0.7974 (t0) cc_final: 0.7600 (t0) REVERT: A 245 MET cc_start: 0.6897 (mmm) cc_final: 0.6408 (ttm) REVERT: A 256 SER cc_start: 0.7923 (t) cc_final: 0.7558 (p) REVERT: A 517 TYR cc_start: 0.8655 (t80) cc_final: 0.8425 (t80) REVERT: A 632 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 1145 TRP cc_start: 0.7424 (m-10) cc_final: 0.7216 (m-10) REVERT: A 1305 ASP cc_start: 0.8221 (t0) cc_final: 0.7833 (t70) REVERT: A 1341 ASP cc_start: 0.8628 (t0) cc_final: 0.7894 (m-30) REVERT: A 1429 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8391 (mtpp) outliers start: 5 outliers final: 4 residues processed: 120 average time/residue: 0.2385 time to fit residues: 40.2918 Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [43, 66, 59, 25, 26, 37, 88, 0, 27, 109, 68] chunk 43 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119123 restraints weight = 64751.756| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.66 r_work: 0.3284 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10200 Z= 0.096 Angle : 0.437 6.189 13845 Z= 0.230 Chirality : 0.035 0.137 1607 Planarity : 0.003 0.050 1600 Dihedral : 11.820 145.714 2402 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.49 % Allowed : 7.70 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.65 (0.26), residues: 1152 helix: 2.37 (0.20), residues: 732 sheet: -1.62 (0.60), residues: 58 loop : -1.20 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 933 TYR 0.005 0.001 TYR A 304 PHE 0.008 0.001 PHE A1107 TRP 0.019 0.001 TRP A1274 HIS 0.003 0.001 HIS A1402 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (10200) covalent geometry : angle 0.43722 / 0.23 (13845) hydrogen bonds : bond 0.03686 / 2.45 ( 545) hydrogen bonds : angle 3.75928 / 2.63 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.428 Fit side-chains REVERT: A 44 ASP cc_start: 0.7863 (t0) cc_final: 0.7544 (t0) REVERT: A 245 MET cc_start: 0.6711 (mmm) cc_final: 0.6188 (ttm) REVERT: A 256 SER cc_start: 0.7864 (t) cc_final: 0.7505 (p) REVERT: A 632 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 1305 ASP cc_start: 0.7983 (t0) cc_final: 0.7498 (t0) REVERT: A 1341 ASP cc_start: 0.8579 (t0) cc_final: 0.7839 (m-30) REVERT: A 1429 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8431 (mtpp) outliers start: 5 outliers final: 5 residues processed: 129 average time/residue: 0.2202 time to fit residues: 40.2444 Evaluate side-chains 123 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [57, 46, 104, 67, 5, 72, 87, 88, 103, 32, 39] chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114288 restraints weight = 71358.037| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.80 r_work: 0.3221 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10200 Z= 0.210 Angle : 0.527 6.321 13845 Z= 0.279 Chirality : 0.038 0.154 1607 Planarity : 0.004 0.051 1600 Dihedral : 12.231 145.501 2402 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.59 % Allowed : 8.00 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.10 (0.26), residues: 1152 helix: 2.00 (0.20), residues: 747 sheet: -2.51 (0.56), residues: 66 loop : -1.53 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1301 TYR 0.010 0.001 TYR A 563 PHE 0.017 0.001 PHE A1300 TRP 0.031 0.001 TRP A1274 HIS 0.007 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (10200) covalent geometry : angle 0.52717 / 0.28 (13845) hydrogen bonds : bond 0.04477 / 2.98 ( 545) hydrogen bonds : angle 3.95230 / 2.76 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.395 Fit side-chains REVERT: A 44 ASP cc_start: 0.8010 (t0) cc_final: 0.7664 (t0) REVERT: A 245 MET cc_start: 0.6950 (mmm) cc_final: 0.6461 (ttm) REVERT: A 256 SER cc_start: 0.7987 (t) cc_final: 0.7616 (p) REVERT: A 632 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 1341 ASP cc_start: 0.8647 (t0) cc_final: 0.7915 (m-30) outliers start: 6 outliers final: 5 residues processed: 120 average time/residue: 0.2386 time to fit residues: 39.5966 Evaluate side-chains 119 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [29, 110, 102, 90, 69, 81, 84, 82, 39, 23, 58] chunk 29 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115839 restraints weight = 73714.772| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.83 r_work: 0.3248 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10200 Z= 0.109 Angle : 0.460 7.981 13845 Z= 0.241 Chirality : 0.035 0.134 1607 Planarity : 0.003 0.050 1600 Dihedral : 11.816 145.729 2402 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.49 % Allowed : 8.09 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.46 (0.26), residues: 1152 helix: 2.27 (0.20), residues: 737 sheet: -2.37 (0.55), residues: 66 loop : -1.25 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1066 TYR 0.006 0.001 TYR A 380 PHE 0.008 0.001 PHE A 490 TRP 0.024 0.001 TRP A1274 HIS 0.003 0.001 HIS A1402 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10200) covalent geometry : angle 0.46045 / 0.24 (13845) hydrogen bonds : bond 0.03885 / 2.58 ( 545) hydrogen bonds : angle 3.80623 / 2.66 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1251 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.576 Fit side-chains REVERT: A 44 ASP cc_start: 0.7909 (t0) cc_final: 0.7566 (t0) REVERT: A 245 MET cc_start: 0.6814 (mmm) cc_final: 0.6376 (ttm) REVERT: A 256 SER cc_start: 0.7893 (t) cc_final: 0.7533 (p) REVERT: A 632 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 1305 ASP cc_start: 0.8053 (t0) cc_final: 0.7570 (t0) REVERT: A 1341 ASP cc_start: 0.8617 (t0) cc_final: 0.7899 (m-30) outliers start: 5 outliers final: 5 residues processed: 122 average time/residue: 0.2277 time to fit residues: 39.8471 Evaluate side-chains 120 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 932 PHE Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1274 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [66, 104, 103, 36, 69, 91, 35, 74, 71, 64, 23] chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114906 restraints weight = 71893.528| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.89 r_work: 0.3259 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10200 Z= 0.125 Angle : 0.460 6.231 13845 Z= 0.243 Chirality : 0.036 0.134 1607 Planarity : 0.003 0.050 1600 Dihedral : 11.703 145.975 2402 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.49 % Allowed : 8.19 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.48 (0.26), residues: 1152 helix: 2.28 (0.20), residues: 737 sheet: -2.39 (0.55), residues: 66 loop : -1.22 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.007 0.001 TYR A 517 PHE 0.008 0.001 PHE A1116 TRP 0.024 0.001 TRP A1274 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10200) covalent geometry : angle 0.46017 / 0.24 (13845) hydrogen bonds : bond 0.03915 / 2.60 ( 545) hydrogen bonds : angle 3.80411 / 2.66 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4652.92 seconds wall clock time: 79 minutes 28.91 seconds (4768.91 seconds total)