Starting phenix.real_space_refine on Wed Apr 30 19:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.map" model { file = "/net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw5_47236/04_2025/9dw5_47236.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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 4 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 6231 2.51 5 N 1733 2.21 5 O 1749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9748 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 7709 Classifications: {'peptide': 1134} Incomplete info: {'truncation_to_alanine': 404} Link IDs: {'PTRANS': 28, 'TRANS': 1105} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1437 Unresolved non-hydrogen angles: 1830 Unresolved non-hydrogen dihedrals: 1192 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 21, 'GLU:plan': 35, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 747 Chain: "G" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2006 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 14, 'TRANS': 315} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 760 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 646 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 11, 'TPO:plan-1': 1, 'ARG:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 11, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 421 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: 7.53, per 1000 atoms: 0.77 Number of scatterers: 9748 At special positions: 0 Unit cell: (106.132, 135.876, 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 29 16.00 P 4 15.00 Mg 2 11.99 O 1749 8.00 N 1733 7.00 C 6231 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: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2750 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 65.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.722A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.145A 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 64 removed outlier: 3.539A pdb=" N LYS A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 98 removed outlier: 4.187A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.632A pdb=" N LEU A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 108 No H-bonds generated for 'chain 'A' and resid 107 through 108' Processing helix chain 'A' and resid 118 through 118 No H-bonds generated for 'chain 'A' and resid 118 through 118' Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.540A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.559A pdb=" N GLY A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.568A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.341A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.624A pdb=" N ALA A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 223 through 268 removed outlier: 3.515A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 329 removed outlier: 4.460A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.229A pdb=" N THR A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 352 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 375 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.622A pdb=" N PHE A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.978A pdb=" N ASP A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.927A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.657A pdb=" N GLY A 576 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 578 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 578' Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.604A pdb=" N LYS A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 4.269A pdb=" N GLN A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 845 through 854 Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.168A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 916 through 922 removed outlier: 3.799A pdb=" N VAL A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 930 through 957 removed outlier: 4.137A pdb=" N LEU A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) Proline residue: A 936 - end of helix Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.572A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 978 removed outlier: 3.918A pdb=" N LEU A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.227A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1047 Proline residue: A1021 - end of helix removed outlier: 3.957A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1069 removed outlier: 3.931A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TRP A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.900A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1168 removed outlier: 3.612A pdb=" N GLY A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.592A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1285 removed outlier: 3.832A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.757A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.773A pdb=" N CYS A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1363 Processing helix chain 'A' and resid 1371 through 1376 removed outlier: 4.115A pdb=" N HIS A1375 " --> pdb=" O GLU A1371 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A1376 " --> pdb=" O PRO A1372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1371 through 1376' Processing helix chain 'A' and resid 1377 through 1391 Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 3.682A pdb=" N MET A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.552A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (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: 3.686A pdb=" N HIS G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 161 removed outlier: 3.854A pdb=" N GLN G 150 " --> pdb=" O PHE G 146 " (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 207 through 212 Processing helix chain 'G' and resid 219 through 235 removed outlier: 3.763A pdb=" N TRP G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 224 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR G 230 " --> pdb=" O GLY G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 254 Processing helix chain 'G' and resid 263 through 274 removed outlier: 3.591A pdb=" N ARG G 271 " --> pdb=" O LYS G 267 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) 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 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 397 removed outlier: 3.515A pdb=" N VAL A 392 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 600 through 603 removed outlier: 3.573A pdb=" N LEU A 454 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 1228 through 1234 removed outlier: 7.327A pdb=" N GLU A1228 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1216 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1214 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A1210 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL A1212 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN A1268 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A1262 " --> pdb=" O LYS A1218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1240 through 1242 Processing sheet with id=AA6, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 7.471A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A1367 " --> pdb=" O THR A1396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.783A pdb=" N LYS G 48 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET G 119 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE G 109 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU G 122 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU G 107 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 173 through 175 640 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.05 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: 3283 1.34 - 1.46: 2335 1.46 - 1.58: 4231 1.58 - 1.71: 3 1.71 - 1.83: 55 Bond restraints: 9907 Sorted by residual: bond pdb=" C5 ANP G 403 " pdb=" N7 ANP G 403 " ideal model delta sigma weight residual 1.370 1.532 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C6 ANP G 403 " pdb=" N6 ANP G 403 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C4 ANP G 403 " pdb=" N9 ANP G 403 " ideal model delta sigma weight residual 1.363 1.222 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C8 ANP G 403 " pdb=" N9 ANP G 403 " ideal model delta sigma weight residual 1.369 1.250 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C1' ANP G 403 " pdb=" O4' ANP G 403 " ideal model delta sigma weight residual 1.394 1.503 -0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 9902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 13471 3.80 - 7.60: 61 7.60 - 11.40: 13 11.40 - 15.20: 3 15.20 - 19.00: 3 Bond angle restraints: 13551 Sorted by residual: angle pdb=" O1B ANP G 403 " pdb=" PB ANP G 403 " pdb=" O2B ANP G 403 " ideal model delta sigma weight residual 120.08 101.08 19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" O1A ANP G 403 " pdb=" PA ANP G 403 " pdb=" O2A ANP G 403 " ideal model delta sigma weight residual 120.18 101.23 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C4 ANP G 403 " pdb=" N9 ANP G 403 " pdb=" C8 ANP G 403 " ideal model delta sigma weight residual 106.24 122.96 -16.72 3.00e+00 1.11e-01 3.10e+01 angle pdb=" N3B ANP G 403 " pdb=" PG ANP G 403 " pdb=" O2G ANP G 403 " ideal model delta sigma weight residual 101.05 114.35 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O3A ANP G 403 " pdb=" PA ANP G 403 " pdb=" O5' ANP G 403 " ideal model delta sigma weight residual 98.09 110.51 -12.42 3.00e+00 1.11e-01 1.71e+01 ... (remaining 13546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5244 17.40 - 34.80: 400 34.80 - 52.21: 120 52.21 - 69.61: 12 69.61 - 87.01: 6 Dihedral angle restraints: 5782 sinusoidal: 1550 harmonic: 4232 Sorted by residual: dihedral pdb=" CA GLU A 384 " pdb=" C GLU A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CG ARG A1128 " pdb=" CD ARG A1128 " pdb=" NE ARG A1128 " pdb=" CZ ARG A1128 " ideal model delta sinusoidal sigma weight residual 180.00 -137.41 -42.59 2 1.50e+01 4.44e-03 9.77e+00 dihedral pdb=" CA ILE A 972 " pdb=" CB ILE A 972 " pdb=" CG1 ILE A 972 " pdb=" CD1 ILE A 972 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 5779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1332 0.049 - 0.099: 283 0.099 - 0.148: 39 0.148 - 0.198: 2 0.198 - 0.247: 1 Chirality restraints: 1657 Sorted by residual: 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 -2.48 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU A 235 " pdb=" CB LEU A 235 " pdb=" CD1 LEU A 235 " pdb=" CD2 LEU A 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CG LEU A 53 " pdb=" CB LEU A 53 " pdb=" CD1 LEU A 53 " pdb=" CD2 LEU A 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 1654 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1139 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ILE A1139 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE A1139 " 0.008 2.00e-02 2.50e+03 pdb=" N MET A1140 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 139 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 140 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1107 " -0.010 2.00e-02 2.50e+03 8.12e-03 1.15e+00 pdb=" CG PHE A1107 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A1107 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A1107 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1107 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1107 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1107 " -0.002 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 50 2.59 - 3.17: 8325 3.17 - 3.74: 15207 3.74 - 4.32: 17509 4.32 - 4.90: 30073 Nonbonded interactions: 71164 Sorted by model distance: nonbonded pdb="MG MG G 401 " pdb=" O1B ANP G 403 " model vdw 2.012 2.170 nonbonded pdb="MG MG G 401 " pdb=" O3G ANP G 403 " model vdw 2.014 2.170 nonbonded pdb="MG MG G 402 " pdb=" O2G ANP G 403 " model vdw 2.053 2.170 nonbonded pdb="MG MG G 401 " pdb=" N3B ANP G 403 " model vdw 2.086 2.250 nonbonded pdb="MG MG G 402 " pdb=" N3B ANP G 403 " model vdw 2.098 2.250 ... (remaining 71159 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: 54.740 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 9907 Z= 0.245 Angle : 0.759 18.997 13551 Z= 0.366 Chirality : 0.040 0.247 1657 Planarity : 0.003 0.032 1748 Dihedral : 14.406 87.009 3032 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 2.49 % Allowed : 23.54 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1443 helix: 1.62 (0.18), residues: 856 sheet: -2.25 (0.44), residues: 100 loop : -0.68 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 865 HIS 0.002 0.000 HIS A 147 PHE 0.018 0.001 PHE A1107 TYR 0.010 0.001 TYR A 161 ARG 0.005 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.15483 ( 640) hydrogen bonds : angle 5.54757 ( 1893) covalent geometry : bond 0.00478 ( 9907) covalent geometry : angle 0.75868 (13551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8060 (pp20) cc_final: 0.7398 (tp30) REVERT: A 229 PHE cc_start: 0.8208 (t80) cc_final: 0.7626 (t80) REVERT: A 244 MET cc_start: 0.9494 (ttm) cc_final: 0.9268 (ttm) REVERT: A 948 LEU cc_start: 0.9066 (tp) cc_final: 0.8784 (tp) REVERT: A 961 MET cc_start: 0.8381 (tpp) cc_final: 0.8144 (tpp) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.1667 time to fit residues: 38.4423 Evaluate side-chains 140 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.112617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089105 restraints weight = 30005.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090308 restraints weight = 15588.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090569 restraints weight = 10628.863| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9907 Z= 0.178 Angle : 0.567 9.348 13551 Z= 0.294 Chirality : 0.041 0.142 1657 Planarity : 0.003 0.039 1748 Dihedral : 5.326 54.575 1578 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 6.14 % Allowed : 20.32 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1443 helix: 1.38 (0.18), residues: 895 sheet: -2.87 (0.50), residues: 76 loop : -0.78 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 303 HIS 0.004 0.001 HIS A 146 PHE 0.010 0.001 PHE A1107 TYR 0.008 0.001 TYR G 157 ARG 0.003 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 640) hydrogen bonds : angle 4.62400 ( 1893) covalent geometry : bond 0.00400 ( 9907) covalent geometry : angle 0.56694 (13551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8380 (pp20) cc_final: 0.7723 (tp30) REVERT: A 54 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 55 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8311 (ptm160) REVERT: A 224 PHE cc_start: 0.8072 (m-80) cc_final: 0.6871 (p90) REVERT: A 229 PHE cc_start: 0.8338 (t80) cc_final: 0.7731 (t80) REVERT: A 244 MET cc_start: 0.9513 (ttm) cc_final: 0.9162 (ttm) REVERT: A 869 ILE cc_start: 0.9311 (mm) cc_final: 0.8810 (mm) REVERT: A 926 LEU cc_start: 0.8883 (tp) cc_final: 0.8623 (tp) REVERT: A 961 MET cc_start: 0.8336 (tpp) cc_final: 0.8067 (tpp) outliers start: 42 outliers final: 30 residues processed: 162 average time/residue: 0.1584 time to fit residues: 39.6984 Evaluate side-chains 153 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 133 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.109785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084071 restraints weight = 30109.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086453 restraints weight = 15667.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088129 restraints weight = 10257.319| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9907 Z= 0.116 Angle : 0.512 10.819 13551 Z= 0.261 Chirality : 0.039 0.180 1657 Planarity : 0.003 0.034 1748 Dihedral : 4.357 51.954 1566 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 5.85 % Allowed : 20.91 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1443 helix: 1.53 (0.18), residues: 888 sheet: -2.66 (0.48), residues: 87 loop : -0.72 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 303 HIS 0.002 0.000 HIS A1054 PHE 0.012 0.001 PHE A1107 TYR 0.009 0.001 TYR A 161 ARG 0.004 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 640) hydrogen bonds : angle 4.20333 ( 1893) covalent geometry : bond 0.00240 ( 9907) covalent geometry : angle 0.51214 (13551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8401 (pp20) cc_final: 0.7672 (tp30) REVERT: A 54 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 55 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8101 (ptm160) REVERT: A 229 PHE cc_start: 0.8165 (t80) cc_final: 0.7551 (t80) REVERT: A 244 MET cc_start: 0.9429 (ttm) cc_final: 0.9103 (ttm) REVERT: A 346 LEU cc_start: 0.8941 (tp) cc_final: 0.8696 (tt) REVERT: A 948 LEU cc_start: 0.9085 (tp) cc_final: 0.8872 (tp) REVERT: A 961 MET cc_start: 0.8336 (tpp) cc_final: 0.8082 (tpp) outliers start: 40 outliers final: 30 residues processed: 162 average time/residue: 0.1594 time to fit residues: 39.9313 Evaluate side-chains 160 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 143 HIS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 0.1980 chunk 92 optimal weight: 20.0000 chunk 39 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 overall best weight: 1.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.108189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082675 restraints weight = 29980.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.085003 restraints weight = 15766.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086607 restraints weight = 10409.956| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9907 Z= 0.156 Angle : 0.542 8.972 13551 Z= 0.278 Chirality : 0.040 0.126 1657 Planarity : 0.003 0.037 1748 Dihedral : 4.278 51.259 1565 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 7.31 % Allowed : 20.76 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1443 helix: 1.57 (0.18), residues: 889 sheet: -2.61 (0.49), residues: 85 loop : -0.94 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 865 HIS 0.003 0.001 HIS A 146 PHE 0.009 0.001 PHE A1107 TYR 0.009 0.001 TYR G 157 ARG 0.005 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 640) hydrogen bonds : angle 4.19574 ( 1893) covalent geometry : bond 0.00353 ( 9907) covalent geometry : angle 0.54203 (13551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8481 (pp20) cc_final: 0.7730 (tp30) REVERT: A 54 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 224 PHE cc_start: 0.8058 (m-80) cc_final: 0.6900 (p90) REVERT: A 229 PHE cc_start: 0.8252 (t80) cc_final: 0.7639 (t80) REVERT: A 244 MET cc_start: 0.9427 (ttm) cc_final: 0.9127 (ttm) REVERT: A 346 LEU cc_start: 0.8990 (tp) cc_final: 0.8749 (tt) REVERT: A 869 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8843 (tt) REVERT: A 948 LEU cc_start: 0.9094 (tp) cc_final: 0.8837 (tp) REVERT: A 961 MET cc_start: 0.8372 (tpp) cc_final: 0.8086 (tpp) REVERT: A 1169 MET cc_start: 0.8092 (tpt) cc_final: 0.7683 (ttm) REVERT: G 129 MET cc_start: 0.7866 (tmm) cc_final: 0.7436 (tmm) outliers start: 50 outliers final: 37 residues processed: 164 average time/residue: 0.1458 time to fit residues: 37.8779 Evaluate side-chains 162 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 143 HIS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 3 optimal weight: 2.9990 chunk 103 optimal weight: 50.0000 chunk 126 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.108637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083029 restraints weight = 29892.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085362 restraints weight = 15747.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086972 restraints weight = 10389.404| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9907 Z= 0.131 Angle : 0.537 11.992 13551 Z= 0.271 Chirality : 0.040 0.176 1657 Planarity : 0.003 0.037 1748 Dihedral : 4.207 49.163 1565 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 7.60 % Allowed : 21.64 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1443 helix: 1.62 (0.18), residues: 888 sheet: -2.21 (0.50), residues: 91 loop : -0.89 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 865 HIS 0.003 0.001 HIS A1054 PHE 0.010 0.001 PHE A 932 TYR 0.009 0.001 TYR G 157 ARG 0.003 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 640) hydrogen bonds : angle 4.06217 ( 1893) covalent geometry : bond 0.00289 ( 9907) covalent geometry : angle 0.53682 (13551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8433 (pp20) cc_final: 0.7693 (tp30) REVERT: A 54 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 55 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8412 (ptm160) REVERT: A 224 PHE cc_start: 0.8063 (m-80) cc_final: 0.6893 (p90) REVERT: A 229 PHE cc_start: 0.8193 (t80) cc_final: 0.7594 (t80) REVERT: A 244 MET cc_start: 0.9432 (ttm) cc_final: 0.9060 (ttm) REVERT: A 303 ARG cc_start: 0.8770 (tpm170) cc_final: 0.8505 (tpm170) REVERT: A 346 LEU cc_start: 0.8992 (tp) cc_final: 0.8757 (tt) REVERT: A 948 LEU cc_start: 0.9103 (tp) cc_final: 0.8861 (tp) REVERT: A 961 MET cc_start: 0.8332 (tpp) cc_final: 0.8059 (tpp) REVERT: G 129 MET cc_start: 0.7874 (tmm) cc_final: 0.7401 (tmm) outliers start: 52 outliers final: 41 residues processed: 165 average time/residue: 0.1782 time to fit residues: 45.1839 Evaluate side-chains 167 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 143 HIS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083993 restraints weight = 29997.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086381 restraints weight = 15615.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.088022 restraints weight = 10236.956| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9907 Z= 0.113 Angle : 0.529 9.445 13551 Z= 0.264 Chirality : 0.039 0.189 1657 Planarity : 0.003 0.035 1748 Dihedral : 4.083 47.815 1565 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 6.58 % Allowed : 22.08 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1443 helix: 1.72 (0.18), residues: 888 sheet: -2.46 (0.52), residues: 83 loop : -0.82 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 865 HIS 0.002 0.000 HIS A1054 PHE 0.011 0.001 PHE A1107 TYR 0.011 0.001 TYR G 157 ARG 0.007 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 640) hydrogen bonds : angle 3.90177 ( 1893) covalent geometry : bond 0.00240 ( 9907) covalent geometry : angle 0.52908 (13551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8377 (pp20) cc_final: 0.7634 (tp30) REVERT: A 55 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8463 (ptm160) REVERT: A 224 PHE cc_start: 0.7996 (m-80) cc_final: 0.6837 (p90) REVERT: A 229 PHE cc_start: 0.8167 (t80) cc_final: 0.7527 (t80) REVERT: A 243 MET cc_start: 0.8756 (mmm) cc_final: 0.8533 (mmm) REVERT: A 244 MET cc_start: 0.9381 (ttm) cc_final: 0.9081 (ttm) REVERT: A 303 ARG cc_start: 0.8792 (tpm170) cc_final: 0.8382 (tpm170) REVERT: A 346 LEU cc_start: 0.8971 (tp) cc_final: 0.8736 (tt) REVERT: A 873 GLU cc_start: 0.8679 (pt0) cc_final: 0.8351 (tm-30) REVERT: A 948 LEU cc_start: 0.9096 (tp) cc_final: 0.8863 (tp) REVERT: A 961 MET cc_start: 0.8266 (tpp) cc_final: 0.7995 (tpp) REVERT: A 1048 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8142 (tmm-80) REVERT: G 129 MET cc_start: 0.7849 (tmm) cc_final: 0.7349 (tmm) outliers start: 45 outliers final: 30 residues processed: 165 average time/residue: 0.1701 time to fit residues: 42.8396 Evaluate side-chains 157 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 0.0050 chunk 139 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.109559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084491 restraints weight = 30128.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086931 restraints weight = 15548.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088609 restraints weight = 10092.506| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9907 Z= 0.115 Angle : 0.541 11.815 13551 Z= 0.269 Chirality : 0.040 0.199 1657 Planarity : 0.003 0.033 1748 Dihedral : 3.688 27.912 1561 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.56 % Allowed : 24.12 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1443 helix: 1.72 (0.18), residues: 889 sheet: -2.26 (0.53), residues: 80 loop : -0.89 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 865 HIS 0.002 0.000 HIS A1054 PHE 0.012 0.001 PHE A1107 TYR 0.009 0.001 TYR A 161 ARG 0.005 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 640) hydrogen bonds : angle 3.85341 ( 1893) covalent geometry : bond 0.00244 ( 9907) covalent geometry : angle 0.54095 (13551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8446 (pp20) cc_final: 0.7651 (tp30) REVERT: A 55 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8432 (ptm160) REVERT: A 189 ASN cc_start: 0.7229 (p0) cc_final: 0.7006 (p0) REVERT: A 229 PHE cc_start: 0.8130 (t80) cc_final: 0.7483 (t80) REVERT: A 244 MET cc_start: 0.9391 (ttm) cc_final: 0.9114 (ttm) REVERT: A 873 GLU cc_start: 0.8644 (pt0) cc_final: 0.8364 (tm-30) REVERT: A 948 LEU cc_start: 0.9102 (tp) cc_final: 0.8892 (tp) REVERT: A 961 MET cc_start: 0.8240 (tpp) cc_final: 0.7978 (tpp) outliers start: 38 outliers final: 33 residues processed: 153 average time/residue: 0.1665 time to fit residues: 39.2659 Evaluate side-chains 157 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 chunk 94 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.109117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083660 restraints weight = 30711.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086014 restraints weight = 15954.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087688 restraints weight = 10446.526| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9907 Z= 0.125 Angle : 0.568 10.991 13551 Z= 0.280 Chirality : 0.041 0.274 1657 Planarity : 0.003 0.032 1748 Dihedral : 3.668 27.776 1560 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.14 % Allowed : 23.83 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1443 helix: 1.72 (0.18), residues: 889 sheet: -2.69 (0.54), residues: 74 loop : -0.93 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 865 HIS 0.002 0.001 HIS A1054 PHE 0.014 0.001 PHE G 262 TYR 0.008 0.001 TYR A 161 ARG 0.009 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 640) hydrogen bonds : angle 3.87769 ( 1893) covalent geometry : bond 0.00277 ( 9907) covalent geometry : angle 0.56840 (13551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8428 (pp20) cc_final: 0.7639 (tp30) REVERT: A 55 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8451 (ptm160) REVERT: A 189 ASN cc_start: 0.7234 (p0) cc_final: 0.7012 (p0) REVERT: A 229 PHE cc_start: 0.8135 (t80) cc_final: 0.7491 (t80) REVERT: A 244 MET cc_start: 0.9387 (ttm) cc_final: 0.9071 (ttm) REVERT: A 303 ARG cc_start: 0.8757 (tpm170) cc_final: 0.8486 (tpm170) REVERT: A 873 GLU cc_start: 0.8630 (pt0) cc_final: 0.8407 (tm-30) REVERT: A 948 LEU cc_start: 0.9104 (tp) cc_final: 0.8871 (tp) REVERT: A 961 MET cc_start: 0.8253 (tpp) cc_final: 0.8002 (tpp) outliers start: 42 outliers final: 35 residues processed: 156 average time/residue: 0.1522 time to fit residues: 37.3326 Evaluate side-chains 162 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 7.9990 chunk 115 optimal weight: 50.0000 chunk 91 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 74 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 HIS ** 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 = 0.3778 r_free = 0.3778 target = 0.106540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081263 restraints weight = 30647.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083510 restraints weight = 16098.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085062 restraints weight = 10665.032| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9907 Z= 0.186 Angle : 0.646 12.667 13551 Z= 0.320 Chirality : 0.043 0.287 1657 Planarity : 0.003 0.035 1748 Dihedral : 3.978 29.458 1560 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.43 % Allowed : 23.68 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1443 helix: 1.61 (0.18), residues: 878 sheet: -2.83 (0.54), residues: 77 loop : -0.96 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 865 HIS 0.004 0.001 HIS A1054 PHE 0.018 0.001 PHE G 262 TYR 0.009 0.001 TYR A 38 ARG 0.007 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 640) hydrogen bonds : angle 4.15250 ( 1893) covalent geometry : bond 0.00424 ( 9907) covalent geometry : angle 0.64589 (13551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8515 (pp20) cc_final: 0.7750 (tp30) REVERT: A 54 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7716 (tm-30) REVERT: A 55 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8410 (ptm160) REVERT: A 224 PHE cc_start: 0.8208 (m-80) cc_final: 0.6972 (p90) REVERT: A 229 PHE cc_start: 0.8240 (t80) cc_final: 0.7626 (t80) REVERT: A 244 MET cc_start: 0.9411 (ttm) cc_final: 0.9182 (ttm) REVERT: A 948 LEU cc_start: 0.9125 (tp) cc_final: 0.8836 (tp) REVERT: A 961 MET cc_start: 0.8298 (tpp) cc_final: 0.8031 (tpp) REVERT: A 983 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 1048 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8305 (tmm-80) outliers start: 44 outliers final: 34 residues processed: 158 average time/residue: 0.1684 time to fit residues: 40.9023 Evaluate side-chains 159 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 chunk 138 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 HIS ** 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 = 0.3818 r_free = 0.3818 target = 0.109040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084110 restraints weight = 30101.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086519 restraints weight = 15468.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.088180 restraints weight = 10073.016| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9907 Z= 0.117 Angle : 0.611 13.982 13551 Z= 0.295 Chirality : 0.041 0.265 1657 Planarity : 0.003 0.029 1748 Dihedral : 3.747 28.494 1560 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.09 % Allowed : 26.32 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1443 helix: 1.72 (0.18), residues: 883 sheet: -2.25 (0.54), residues: 80 loop : -0.91 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 303 HIS 0.002 0.000 HIS A1054 PHE 0.015 0.001 PHE A1107 TYR 0.009 0.001 TYR A 161 ARG 0.006 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 640) hydrogen bonds : angle 3.89615 ( 1893) covalent geometry : bond 0.00245 ( 9907) covalent geometry : angle 0.61082 (13551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.8778 (tt) cc_final: 0.8499 (mp) REVERT: A 51 GLU cc_start: 0.8443 (pp20) cc_final: 0.7661 (tp30) REVERT: A 54 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7669 (tm-30) REVERT: A 55 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8378 (ptm160) REVERT: A 224 PHE cc_start: 0.8144 (m-80) cc_final: 0.6920 (p90) REVERT: A 229 PHE cc_start: 0.8179 (t80) cc_final: 0.7554 (t80) REVERT: A 244 MET cc_start: 0.9435 (ttm) cc_final: 0.9141 (ttm) REVERT: A 251 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8308 (ttm-80) REVERT: A 948 LEU cc_start: 0.9096 (tp) cc_final: 0.8858 (tp) REVERT: A 961 MET cc_start: 0.8204 (tpp) cc_final: 0.7931 (tpp) REVERT: A 1048 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8280 (tmm-80) outliers start: 28 outliers final: 25 residues processed: 149 average time/residue: 0.1886 time to fit residues: 43.2351 Evaluate side-chains 155 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 945 SER Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 101 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 HIS ** 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 = 0.3796 r_free = 0.3796 target = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082374 restraints weight = 30288.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084685 restraints weight = 16031.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.086285 restraints weight = 10564.232| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9907 Z= 0.150 Angle : 0.632 13.367 13551 Z= 0.309 Chirality : 0.042 0.276 1657 Planarity : 0.003 0.031 1748 Dihedral : 3.817 28.534 1560 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.39 % Allowed : 25.88 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1443 helix: 1.72 (0.18), residues: 888 sheet: -2.30 (0.54), residues: 80 loop : -0.99 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 PHE 0.014 0.001 PHE G 262 TYR 0.009 0.001 TYR A 38 ARG 0.006 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 640) hydrogen bonds : angle 4.01327 ( 1893) covalent geometry : bond 0.00338 ( 9907) covalent geometry : angle 0.63150 (13551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.30 seconds wall clock time: 69 minutes 9.00 seconds (4149.00 seconds total)