Starting phenix.real_space_refine on Fri Jul 3 04:21:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.map" model { file = "/net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw8_47238/07_2026/9dw8_47238.cif" } resolution = 3.5 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= 0.002 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 56 5.16 5 C 7820 2.51 5 N 2002 2.21 5 O 2134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9452 Classifications: {'peptide': 1182} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 31, 'TRANS': 1150} Chain breaks: 6 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2461 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'PHE:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 2, 'B44': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12026 At special positions: 0 Unit cell: (72.332, 130.468, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 10 15.00 Mg 4 11.99 O 2134 8.00 N 2002 7.00 C 7820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 533.7 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2806 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 10 sheets defined 63.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.557A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.589A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.705A pdb=" N ILE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.507A pdb=" N SER A 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 64 removed outlier: 3.623A pdb=" N GLU A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 97 removed outlier: 8.300A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.818A pdb=" N LEU A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.565A pdb=" N SER A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.656A pdb=" N LEU A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.597A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.173A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.508A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.562A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.573A pdb=" N ILE A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.797A pdb=" N LEU A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 268 removed outlier: 3.869A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 308 removed outlier: 3.554A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.601A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.663A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.502A pdb=" N GLY A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.692A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 513 through 524 removed outlier: 3.620A pdb=" N TYR A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.504A pdb=" N SER A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.533A 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 608 through 613 removed outlier: 4.082A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 3.798A pdb=" N GLN A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 856 through 883 removed outlier: 4.262A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.535A pdb=" N SER A 912 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 927 removed outlier: 3.852A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 959 Proline residue: A 936 - end of helix removed outlier: 4.033A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.685A pdb=" N ASN A 965 " --> pdb=" O MET A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.855A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.461A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN A1012 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1019 through 1047 removed outlier: 3.713A pdb=" N ARG A1030 " --> pdb=" O PHE A1026 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.820A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A1061 " --> pdb=" O THR A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.773A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A1092 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.572A pdb=" N ILE A1132 " --> pdb=" O ARG A1128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1157 removed outlier: 4.379A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1168 removed outlier: 4.021A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1257 removed outlier: 3.685A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1272 Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1315 through 1320 removed outlier: 3.549A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.530A pdb=" N LYS A1351 " --> pdb=" O SER A1347 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 5.321A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.905A pdb=" N GLU A1409 " --> pdb=" O ALA A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.845A pdb=" N LEU A1430 " --> pdb=" O SER A1426 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1431 " --> pdb=" O ILE A1427 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A1432 " --> pdb=" O GLN A1428 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1426 through 1433' Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1442 through 1450 Processing helix chain 'G' and resid 16 through 33 removed outlier: 3.756A pdb=" N LEU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 86 through 99 Processing helix chain 'G' and resid 128 through 137 removed outlier: 3.844A pdb=" N HIS G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 161 removed outlier: 3.937A pdb=" N TYR G 147 " --> pdb=" O HIS G 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN G 150 " --> pdb=" O PHE G 146 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 161 " --> pdb=" O TYR G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 202 through 206 Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'G' and resid 219 through 235 removed outlier: 3.735A pdb=" N TRP G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 254 Processing helix chain 'G' and resid 263 through 274 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 302 through 308 removed outlier: 3.570A pdb=" N GLN G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 6.818A pdb=" N ILE A 331 " --> pdb=" O ILE A 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 449 removed outlier: 6.731A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 395 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 481 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.539A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 454 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA5, first strand: chain 'A' and resid 1233 through 1234 removed outlier: 5.660A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.679A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP A1370 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1240 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1298 through 1299 Processing sheet with id=AA8, first strand: chain 'G' and resid 48 through 49 removed outlier: 4.252A pdb=" N LYS G 48 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR G 118 " --> pdb=" O PHE G 111 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE G 109 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU G 122 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU G 107 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'G' and resid 173 through 175 584 hydrogen bonds defined for protein. 1701 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: 1.74 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3531 1.34 - 1.45: 1868 1.45 - 1.57: 6779 1.57 - 1.69: 13 1.69 - 1.81: 98 Bond restraints: 12289 Sorted by residual: bond pdb=" C8 B44 A1501 " pdb=" N7 B44 A1501 " ideal model delta sigma weight residual 1.369 1.519 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C8 B44 A1502 " pdb=" N7 B44 A1502 " ideal model delta sigma weight residual 1.369 1.516 -0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C5 ANP G 403 " pdb=" N7 ANP G 403 " ideal model delta sigma weight residual 1.370 1.514 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C12 B44 A1501 " pdb=" C14 B44 A1501 " ideal model delta sigma weight residual 1.395 1.531 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C12 B44 A1502 " pdb=" C14 B44 A1502 " ideal model delta sigma weight residual 1.395 1.531 -0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 12284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 16511 4.08 - 8.16: 85 8.16 - 12.24: 24 12.24 - 16.32: 9 16.32 - 20.40: 6 Bond angle restraints: 16635 Sorted by residual: angle pdb=" O5 B44 A1502 " pdb=" P1 B44 A1502 " pdb=" O8 B44 A1502 " ideal model delta sigma weight residual 121.36 100.96 20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" O5 B44 A1501 " pdb=" P1 B44 A1501 " pdb=" O8 B44 A1501 " ideal model delta sigma weight residual 121.36 101.07 20.29 3.00e+00 1.11e-01 4.57e+01 angle pdb=" O1B ANP G 403 " pdb=" PB ANP G 403 " pdb=" O2B ANP G 403 " ideal model delta sigma weight residual 120.08 100.79 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O1A ANP G 403 " pdb=" PA ANP G 403 " pdb=" O2A ANP G 403 " ideal model delta sigma weight residual 120.18 101.53 18.65 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O6 B44 A1502 " pdb=" P2 B44 A1502 " pdb=" O9 B44 A1502 " ideal model delta sigma weight residual 119.05 100.51 18.54 3.00e+00 1.11e-01 3.82e+01 ... (remaining 16630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.88: 6674 19.88 - 39.77: 531 39.77 - 59.65: 100 59.65 - 79.54: 30 79.54 - 99.42: 17 Dihedral angle restraints: 7352 sinusoidal: 3014 harmonic: 4338 Sorted by residual: dihedral pdb=" CA SER A1311 " pdb=" C SER A1311 " pdb=" N ASP A1312 " pdb=" CA ASP A1312 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ILE A 70 " pdb=" C ILE A 70 " pdb=" N ASN A 71 " pdb=" CA ASN A 71 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LEU A 218 " pdb=" C LEU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1561 0.057 - 0.113: 302 0.113 - 0.170: 25 0.170 - 0.227: 0 0.227 - 0.284: 3 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CB ILE A 70 " pdb=" CA ILE A 70 " pdb=" CG1 ILE A 70 " pdb=" CG2 ILE A 70 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE A1109 " pdb=" CA ILE A1109 " pdb=" CG1 ILE A1109 " pdb=" CG2 ILE A1109 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C2' ANP G 403 " pdb=" C1' ANP G 403 " pdb=" C3' ANP G 403 " pdb=" O2' ANP G 403 " both_signs ideal model delta sigma weight residual False -2.72 -2.49 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1888 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1012 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A1013 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1013 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1013 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1400 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C CYS A1400 " -0.029 2.00e-02 2.50e+03 pdb=" O CYS A1400 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A1401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 319 " -0.008 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE A 319 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 319 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 319 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 319 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 319 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 319 " 0.000 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 22 2.52 - 3.11: 8689 3.11 - 3.71: 17707 3.71 - 4.30: 24304 4.30 - 4.90: 41160 Nonbonded interactions: 91882 Sorted by model distance: nonbonded pdb="MG MG G 401 " pdb=" O3G ANP G 403 " model vdw 1.921 2.170 nonbonded pdb="MG MG G 401 " pdb=" O2B ANP G 403 " model vdw 1.967 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1503 " model vdw 2.061 2.170 nonbonded pdb=" OD2 ASP G 185 " pdb="MG MG G 402 " model vdw 2.309 2.170 nonbonded pdb=" OH TYR A 109 " pdb=" OG SER A1118 " model vdw 2.341 3.040 ... (remaining 91877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.210 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 0.150 12289 Z= 0.339 Angle : 0.935 20.400 16635 Z= 0.418 Chirality : 0.044 0.284 1891 Planarity : 0.003 0.043 2043 Dihedral : 15.878 99.425 4546 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.17 % Allowed : 10.18 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.21), residues: 1470 helix: 0.41 (0.18), residues: 817 sheet: -1.29 (0.51), residues: 92 loop : -1.02 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.024 0.002 TYR A 515 PHE 0.028 0.001 PHE A 319 TRP 0.027 0.002 TRP A1145 HIS 0.015 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.34 (12289) covalent geometry : angle 0.93506 / 0.42 (16635) hydrogen bonds : bond 0.17425 / 11.55 ( 584) hydrogen bonds : angle 5.67322 / 3.92 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.335 Fit side-chains REVERT: A 174 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8301 (mmtp) REVERT: A 600 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (ptt-90) REVERT: A 1152 ASP cc_start: 0.8523 (t0) cc_final: 0.8002 (t0) REVERT: G 59 MET cc_start: 0.6947 (mpp) cc_final: 0.6475 (mmm) REVERT: G 70 TYR cc_start: 0.7950 (m-80) cc_final: 0.7602 (m-10) outliers start: 15 outliers final: 7 residues processed: 131 average time/residue: 0.0862 time to fit residues: 16.9719 Evaluate side-chains 106 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 282 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1291 GLN G 177 GLN G 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093726 restraints weight = 20580.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097242 restraints weight = 10383.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099700 restraints weight = 6644.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101281 restraints weight = 4870.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102461 restraints weight = 3949.011| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12289 Z= 0.150 Angle : 0.583 7.268 16635 Z= 0.300 Chirality : 0.043 0.224 1891 Planarity : 0.004 0.047 2043 Dihedral : 9.780 105.968 1742 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.43 % Allowed : 9.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.22), residues: 1470 helix: 0.87 (0.19), residues: 830 sheet: -0.94 (0.47), residues: 103 loop : -1.16 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 555 TYR 0.012 0.001 TYR A 919 PHE 0.022 0.001 PHE A 81 TRP 0.017 0.001 TRP A1145 HIS 0.011 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (12289) covalent geometry : angle 0.58281 / 0.30 (16635) hydrogen bonds : bond 0.05931 / 3.86 ( 584) hydrogen bonds : angle 4.30377 / 2.97 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.326 Fit side-chains REVERT: A 174 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8422 (mmtp) REVERT: A 583 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 600 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8410 (ptt-90) REVERT: G 59 MET cc_start: 0.6804 (mpp) cc_final: 0.6594 (mmt) REVERT: G 64 MET cc_start: 0.6343 (mmt) cc_final: 0.6094 (mmp) REVERT: G 70 TYR cc_start: 0.7825 (m-80) cc_final: 0.7483 (m-10) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.0852 time to fit residues: 16.6958 Evaluate side-chains 119 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.117660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095076 restraints weight = 20665.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098727 restraints weight = 10374.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101223 restraints weight = 6577.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102908 restraints weight = 4809.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104047 restraints weight = 3868.311| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12289 Z= 0.116 Angle : 0.504 7.295 16635 Z= 0.262 Chirality : 0.041 0.172 1891 Planarity : 0.003 0.051 2043 Dihedral : 8.546 98.549 1736 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.35 % Allowed : 10.02 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1470 helix: 1.09 (0.19), residues: 839 sheet: -0.72 (0.47), residues: 103 loop : -1.10 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 555 TYR 0.010 0.001 TYR A 919 PHE 0.016 0.001 PHE A 81 TRP 0.014 0.001 TRP A 865 HIS 0.008 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12289) covalent geometry : angle 0.50439 / 0.26 (16635) hydrogen bonds : bond 0.04851 / 3.16 ( 584) hydrogen bonds : angle 3.91300 / 2.70 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.487 Fit side-chains REVERT: A 3 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7717 (mmm160) REVERT: A 174 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8325 (mmtp) REVERT: A 583 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 600 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8463 (ptt-90) REVERT: A 883 LEU cc_start: 0.8494 (tt) cc_final: 0.8256 (tt) REVERT: A 1137 MET cc_start: 0.8289 (mmm) cc_final: 0.7887 (mtp) REVERT: G 64 MET cc_start: 0.6362 (mmt) cc_final: 0.6103 (mmp) REVERT: G 70 TYR cc_start: 0.7843 (m-80) cc_final: 0.7515 (m-10) outliers start: 30 outliers final: 18 residues processed: 136 average time/residue: 0.0961 time to fit residues: 19.9393 Evaluate side-chains 123 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094487 restraints weight = 20516.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098058 restraints weight = 10318.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100521 restraints weight = 6549.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102220 restraints weight = 4787.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103255 restraints weight = 3839.268| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12289 Z= 0.120 Angle : 0.492 5.987 16635 Z= 0.257 Chirality : 0.041 0.172 1891 Planarity : 0.003 0.051 2043 Dihedral : 8.144 99.062 1736 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.29 % Allowed : 10.57 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.22), residues: 1470 helix: 1.14 (0.19), residues: 841 sheet: -0.47 (0.48), residues: 98 loop : -1.09 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.013 0.001 TYR A 515 PHE 0.021 0.001 PHE A 319 TRP 0.013 0.001 TRP A 865 HIS 0.008 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12289) covalent geometry : angle 0.49249 / 0.26 (16635) hydrogen bonds : bond 0.04727 / 3.09 ( 584) hydrogen bonds : angle 3.78700 / 2.61 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.519 Fit side-chains REVERT: A 3 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7683 (mmm160) REVERT: A 106 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 174 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8339 (mmtp) REVERT: A 479 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 583 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 600 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8486 (ptt-90) REVERT: A 1137 MET cc_start: 0.8350 (mmm) cc_final: 0.7975 (mmt) REVERT: A 1392 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6268 (p90) REVERT: A 1418 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6257 (pp20) REVERT: G 64 MET cc_start: 0.6343 (mmt) cc_final: 0.6076 (mmp) REVERT: G 70 TYR cc_start: 0.7814 (m-80) cc_final: 0.7549 (m-10) outliers start: 42 outliers final: 25 residues processed: 146 average time/residue: 0.0970 time to fit residues: 21.8216 Evaluate side-chains 132 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1392 PHE Chi-restraints excluded: chain A residue 1418 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 0.0570 chunk 128 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN G 91 ASN ** G 275 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095861 restraints weight = 20422.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099304 restraints weight = 10774.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101668 restraints weight = 7025.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103212 restraints weight = 5221.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104199 restraints weight = 4257.036| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12289 Z= 0.106 Angle : 0.491 9.649 16635 Z= 0.252 Chirality : 0.040 0.180 1891 Planarity : 0.003 0.048 2043 Dihedral : 7.945 100.303 1736 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.05 % Allowed : 11.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1470 helix: 1.23 (0.19), residues: 840 sheet: -0.37 (0.48), residues: 104 loop : -1.10 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.009 0.001 TYR A 919 PHE 0.015 0.001 PHE A 81 TRP 0.012 0.001 TRP A 865 HIS 0.008 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (12289) covalent geometry : angle 0.49149 / 0.25 (16635) hydrogen bonds : bond 0.04393 / 2.86 ( 584) hydrogen bonds : angle 3.70076 / 2.54 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.311 Fit side-chains REVERT: A 3 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7818 (mmm160) REVERT: A 106 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 174 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (mmtp) REVERT: A 479 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8182 (mm-30) REVERT: A 600 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8357 (ptt-90) REVERT: A 1137 MET cc_start: 0.8277 (mmm) cc_final: 0.7979 (mmt) REVERT: A 1392 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6272 (p90) REVERT: G 64 MET cc_start: 0.6482 (mmt) cc_final: 0.6238 (mmp) REVERT: G 70 TYR cc_start: 0.7719 (m-80) cc_final: 0.7430 (m-10) REVERT: G 72 MET cc_start: 0.6206 (ttp) cc_final: 0.5917 (ttt) REVERT: G 282 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8168 (t80) outliers start: 39 outliers final: 25 residues processed: 143 average time/residue: 0.0833 time to fit residues: 18.4968 Evaluate side-chains 136 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1392 PHE Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1419 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 316 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 110 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 143 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN G 91 ASN ** G 275 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.118181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096062 restraints weight = 20264.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099482 restraints weight = 10692.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101818 restraints weight = 6972.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103236 restraints weight = 5188.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104433 restraints weight = 4269.306| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12289 Z= 0.107 Angle : 0.481 8.267 16635 Z= 0.248 Chirality : 0.040 0.191 1891 Planarity : 0.003 0.047 2043 Dihedral : 7.841 100.214 1736 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.05 % Allowed : 12.61 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1470 helix: 1.29 (0.19), residues: 841 sheet: -0.20 (0.48), residues: 104 loop : -1.09 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.014 0.001 TYR A 515 PHE 0.023 0.001 PHE A 319 TRP 0.011 0.001 TRP A 865 HIS 0.008 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (12289) covalent geometry : angle 0.48127 / 0.25 (16635) hydrogen bonds : bond 0.04280 / 2.79 ( 584) hydrogen bonds : angle 3.64369 / 2.50 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.470 Fit side-chains REVERT: A 106 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7458 (mp) REVERT: A 174 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8393 (mmtp) REVERT: A 479 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7968 (mp0) REVERT: A 600 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (ptt-90) REVERT: A 1137 MET cc_start: 0.8264 (mmm) cc_final: 0.7984 (mmt) REVERT: A 1392 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6324 (p90) REVERT: G 70 TYR cc_start: 0.7730 (m-80) cc_final: 0.7445 (m-10) REVERT: G 72 MET cc_start: 0.6221 (ttp) cc_final: 0.5943 (ttt) outliers start: 39 outliers final: 26 residues processed: 142 average time/residue: 0.0836 time to fit residues: 18.5447 Evaluate side-chains 137 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1392 PHE Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 316 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6162 > 50: distance: 23 - 27: 23.516 distance: 27 - 28: 22.168 distance: 28 - 31: 21.333 distance: 29 - 30: 37.215 distance: 29 - 38: 20.188 distance: 31 - 32: 14.274 distance: 32 - 33: 18.415 distance: 32 - 34: 18.179 distance: 33 - 35: 13.553 distance: 34 - 36: 25.939 distance: 35 - 37: 24.436 distance: 36 - 37: 13.852 distance: 38 - 39: 20.251 distance: 39 - 40: 29.195 distance: 39 - 42: 29.970 distance: 40 - 43: 60.637 distance: 43 - 44: 18.345 distance: 44 - 45: 38.509 distance: 45 - 46: 46.141 distance: 45 - 51: 37.818 distance: 47 - 48: 38.878 distance: 48 - 49: 34.229 distance: 48 - 50: 3.803 distance: 51 - 52: 29.726 distance: 52 - 53: 34.861 distance: 52 - 55: 9.497 distance: 53 - 54: 52.687 distance: 53 - 60: 24.048 distance: 54 - 84: 40.390 distance: 56 - 57: 39.318 distance: 57 - 59: 45.057 distance: 60 - 61: 32.313 distance: 60 - 66: 39.565 distance: 61 - 62: 33.813 distance: 61 - 64: 54.464 distance: 62 - 63: 19.674 distance: 62 - 67: 26.842 distance: 63 - 92: 19.779 distance: 64 - 65: 43.804 distance: 65 - 66: 23.908 distance: 67 - 68: 30.059 distance: 68 - 69: 30.843 distance: 68 - 71: 23.939 distance: 69 - 70: 18.249 distance: 69 - 75: 13.766 distance: 70 - 104: 28.597 distance: 71 - 72: 23.300 distance: 71 - 73: 28.364 distance: 72 - 74: 33.871 distance: 75 - 76: 28.958 distance: 76 - 77: 8.131 distance: 76 - 79: 14.576 distance: 77 - 78: 10.740 distance: 77 - 84: 4.378 distance: 78 - 113: 32.689 distance: 79 - 80: 24.168 distance: 80 - 81: 21.332 distance: 81 - 82: 18.279 distance: 81 - 83: 40.331 distance: 84 - 85: 24.268 distance: 85 - 86: 14.715 distance: 85 - 88: 27.171 distance: 86 - 87: 12.597 distance: 86 - 92: 28.730 distance: 87 - 122: 31.721 distance: 88 - 89: 6.167 distance: 88 - 90: 35.028 distance: 89 - 91: 31.617 distance: 92 - 93: 28.064 distance: 93 - 94: 15.103 distance: 93 - 96: 6.944 distance: 94 - 95: 5.077 distance: 94 - 104: 18.990 distance: 95 - 130: 35.201 distance: 96 - 97: 6.976 distance: 97 - 98: 12.997 distance: 97 - 99: 7.055 distance: 98 - 100: 5.355 distance: 99 - 101: 11.193 distance: 100 - 102: 17.514 distance: 101 - 102: 12.004 distance: 102 - 103: 7.473 distance: 104 - 105: 4.335 distance: 105 - 106: 11.204 distance: 106 - 113: 33.174 distance: 107 - 137: 34.024 distance: 108 - 109: 13.466 distance: 109 - 110: 8.411 distance: 110 - 111: 15.396 distance: 110 - 112: 10.754