Starting phenix.real_space_refine on Wed Sep 17 16:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw5_47236/09_2025/9dw5_47236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw5_47236/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dw5_47236/09_2025/9dw5_47236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw5_47236/09_2025/9dw5_47236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dw5_47236/09_2025/9dw5_47236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw5_47236/09_2025/9dw5_47236.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 21, 'GLU:plan': 35, 'TYR:plan': 13, 'ASN:plan1': 14, 'PHE:plan': 21, 'TRP:plan': 6, 'ASP:plan': 22, 'GLN:plan1': 22, 'HIS:plan': 7} 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, 'GLU:plan': 22, 'PHE:plan': 11, 'ASP:plan': 13, 'TRP:plan': 3, 'ASN:plan1': 12, 'HIS:plan': 3, 'ARG:plan': 7, 'TYR:plan': 10, 'TPO:plan-1': 1} 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: 2.53, per 1000 atoms: 0.26 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: 0.96 Conformation dependent library (CDL) restraints added in 373.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.89 Time building geometry restraints manager: 1.18 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: 7.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A1048 TYR 0.010 0.001 TYR A 161 PHE 0.018 0.001 PHE A1107 TRP 0.009 0.001 TRP A 865 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9907) covalent geometry : angle 0.75868 (13551) hydrogen bonds : bond 0.15483 ( 640) hydrogen bonds : angle 5.54757 ( 1893) *********************** 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 : 0.401 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: 0.0726 time to fit residues: 17.2285 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 : 0.378 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.112171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088635 restraints weight = 30340.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089839 restraints weight = 15743.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090065 restraints weight = 10793.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091832 restraints weight = 10184.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091856 restraints weight = 8365.654| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9907 Z= 0.201 Angle : 0.584 9.102 13551 Z= 0.303 Chirality : 0.042 0.149 1657 Planarity : 0.003 0.041 1748 Dihedral : 5.379 54.719 1578 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 6.29 % Allowed : 20.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.23), residues: 1443 helix: 1.33 (0.18), residues: 890 sheet: -2.82 (0.50), residues: 77 loop : -0.80 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.008 0.001 TYR A 325 PHE 0.010 0.001 PHE A1107 TRP 0.008 0.001 TRP A 79 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9907) covalent geometry : angle 0.58406 (13551) hydrogen bonds : bond 0.05418 ( 640) hydrogen bonds : angle 4.65177 ( 1893) *********************** 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 173 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8348 (pp20) cc_final: 0.7695 (tp30) REVERT: A 54 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 55 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8336 (ptm160) REVERT: A 224 PHE cc_start: 0.8044 (m-80) cc_final: 0.6916 (p90) REVERT: A 229 PHE cc_start: 0.8315 (t80) cc_final: 0.7745 (t80) REVERT: A 244 MET cc_start: 0.9520 (ttm) cc_final: 0.9179 (ttm) REVERT: A 869 ILE cc_start: 0.9313 (mm) cc_final: 0.8795 (mm) REVERT: A 926 LEU cc_start: 0.8877 (tp) cc_final: 0.8637 (tp) REVERT: A 961 MET cc_start: 0.8320 (tpp) cc_final: 0.8063 (tpp) outliers start: 43 outliers final: 31 residues processed: 163 average time/residue: 0.0746 time to fit residues: 19.0162 Evaluate side-chains 154 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 1020 VAL 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 134 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 102 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.1796 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081803 restraints weight = 30393.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084122 restraints weight = 15978.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085699 restraints weight = 10588.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086452 restraints weight = 8087.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087320 restraints weight = 6972.849| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9907 Z= 0.172 Angle : 0.555 10.590 13551 Z= 0.286 Chirality : 0.041 0.156 1657 Planarity : 0.003 0.041 1748 Dihedral : 4.664 52.848 1566 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 8.19 % Allowed : 19.44 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.23), residues: 1443 helix: 1.39 (0.18), residues: 883 sheet: -2.69 (0.49), residues: 87 loop : -0.97 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1048 TYR 0.008 0.001 TYR A 38 PHE 0.009 0.001 PHE A1107 TRP 0.006 0.001 TRP A 79 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9907) covalent geometry : angle 0.55519 (13551) hydrogen bonds : bond 0.05189 ( 640) hydrogen bonds : angle 4.41947 ( 1893) *********************** 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 188 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8457 (pp20) cc_final: 0.7724 (tp30) REVERT: A 54 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 55 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8299 (ptm160) REVERT: A 224 PHE cc_start: 0.8056 (m-80) cc_final: 0.6934 (p90) REVERT: A 229 PHE cc_start: 0.8267 (t80) cc_final: 0.7699 (t80) REVERT: A 244 MET cc_start: 0.9459 (ttm) cc_final: 0.9142 (ttm) REVERT: A 346 LEU cc_start: 0.8991 (tp) cc_final: 0.8765 (tt) REVERT: A 948 LEU cc_start: 0.9102 (tp) cc_final: 0.8841 (tp) REVERT: A 961 MET cc_start: 0.8354 (tpp) cc_final: 0.8086 (tpp) REVERT: G 129 MET cc_start: 0.7855 (tmm) cc_final: 0.7287 (tmm) REVERT: G 274 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7718 (tp) outliers start: 56 outliers final: 41 residues processed: 176 average time/residue: 0.0675 time to fit residues: 18.6173 Evaluate side-chains 169 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 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 1001 VAL 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 143 HIS 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 260 SER Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 274 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 92 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 0.0010 chunk 50 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.105462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079667 restraints weight = 30969.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081895 restraints weight = 16382.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083408 restraints weight = 10870.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084143 restraints weight = 8348.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084820 restraints weight = 7222.868| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9907 Z= 0.240 Angle : 0.630 8.317 13551 Z= 0.326 Chirality : 0.042 0.146 1657 Planarity : 0.004 0.047 1748 Dihedral : 4.966 54.176 1566 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 10.38 % Allowed : 18.71 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.23), residues: 1443 helix: 1.28 (0.18), residues: 881 sheet: -2.51 (0.54), residues: 78 loop : -1.17 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1048 TYR 0.009 0.001 TYR A 38 PHE 0.015 0.001 PHE G 258 TRP 0.009 0.001 TRP A 865 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9907) covalent geometry : angle 0.63005 (13551) hydrogen bonds : bond 0.05682 ( 640) hydrogen bonds : angle 4.57343 ( 1893) *********************** 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 200 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8551 (pp20) cc_final: 0.7786 (tp30) REVERT: A 54 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 55 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8301 (ptm160) REVERT: A 189 ASN cc_start: 0.7328 (p0) cc_final: 0.7098 (p0) REVERT: A 212 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7749 (ttt) REVERT: A 224 PHE cc_start: 0.8156 (m-80) cc_final: 0.6979 (p90) REVERT: A 229 PHE cc_start: 0.8358 (t80) cc_final: 0.7807 (t80) REVERT: A 244 MET cc_start: 0.9493 (ttm) cc_final: 0.9250 (ttm) REVERT: A 303 ARG cc_start: 0.8819 (tpm170) cc_final: 0.8442 (tpm170) REVERT: A 320 LEU cc_start: 0.8635 (mp) cc_final: 0.8176 (tt) REVERT: A 948 LEU cc_start: 0.9130 (tp) cc_final: 0.8817 (tp) REVERT: A 961 MET cc_start: 0.8388 (tpp) cc_final: 0.8123 (tpp) REVERT: A 983 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8496 (mp) REVERT: G 129 MET cc_start: 0.7925 (tmm) cc_final: 0.7287 (tmm) outliers start: 71 outliers final: 50 residues processed: 180 average time/residue: 0.0726 time to fit residues: 20.4021 Evaluate side-chains 177 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 86 ILE 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 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 212 MET 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 285 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 845 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 1001 VAL Chi-restraints excluded: chain A residue 1020 VAL 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 1095 THR 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 1143 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 143 HIS 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 260 SER Chi-restraints excluded: chain G residue 262 PHE 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 104 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.107703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081835 restraints weight = 30322.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084139 restraints weight = 15973.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085704 restraints weight = 10556.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086633 restraints weight = 8072.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086936 restraints weight = 6871.160| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9907 Z= 0.129 Angle : 0.539 11.081 13551 Z= 0.273 Chirality : 0.040 0.197 1657 Planarity : 0.003 0.043 1748 Dihedral : 4.628 50.170 1566 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 7.31 % Allowed : 21.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.23), residues: 1443 helix: 1.52 (0.18), residues: 877 sheet: -2.21 (0.51), residues: 91 loop : -0.95 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1048 TYR 0.009 0.001 TYR A 161 PHE 0.011 0.001 PHE A1107 TRP 0.008 0.001 TRP A 865 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9907) covalent geometry : angle 0.53909 (13551) hydrogen bonds : bond 0.04972 ( 640) hydrogen bonds : angle 4.15052 ( 1893) *********************** 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: 50 poor density : 130 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8398 (pp20) cc_final: 0.7664 (tp30) REVERT: A 54 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7229 (tm-30) REVERT: A 55 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8172 (ptm160) REVERT: A 58 ASP cc_start: 0.8030 (p0) cc_final: 0.7798 (p0) REVERT: A 212 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7767 (ttt) REVERT: A 224 PHE cc_start: 0.8106 (m-80) cc_final: 0.6910 (p90) REVERT: A 229 PHE cc_start: 0.8264 (t80) cc_final: 0.7683 (t80) REVERT: A 244 MET cc_start: 0.9418 (ttm) cc_final: 0.9120 (ttm) REVERT: A 303 ARG cc_start: 0.8799 (tpm170) cc_final: 0.8523 (tpm170) REVERT: A 948 LEU cc_start: 0.9104 (tp) cc_final: 0.8863 (tp) REVERT: A 961 MET cc_start: 0.8315 (tpp) cc_final: 0.8055 (tpp) REVERT: A 1048 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8179 (tmm-80) REVERT: G 129 MET cc_start: 0.7947 (tmm) cc_final: 0.7246 (tmm) outliers start: 50 outliers final: 37 residues processed: 164 average time/residue: 0.0713 time to fit residues: 18.0539 Evaluate side-chains 166 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 212 MET 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 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 1058 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1112 ILE 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 143 HIS 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 262 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.108644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083000 restraints weight = 30291.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085317 restraints weight = 15716.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086973 restraints weight = 10318.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.088049 restraints weight = 7848.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.088648 restraints weight = 6578.378| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9907 Z= 0.117 Angle : 0.535 10.718 13551 Z= 0.268 Chirality : 0.039 0.156 1657 Planarity : 0.003 0.042 1748 Dihedral : 4.256 48.983 1564 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.31 % Allowed : 22.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.23), residues: 1443 helix: 1.66 (0.18), residues: 890 sheet: -2.50 (0.53), residues: 83 loop : -0.98 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1048 TYR 0.009 0.001 TYR A 161 PHE 0.012 0.001 PHE A1107 TRP 0.007 0.001 TRP A 865 HIS 0.002 0.000 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9907) covalent geometry : angle 0.53490 (13551) hydrogen bonds : bond 0.04547 ( 640) hydrogen bonds : angle 3.94428 ( 1893) *********************** 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 182 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8417 (pp20) cc_final: 0.7636 (tp30) REVERT: A 54 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7273 (tm-30) REVERT: A 55 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8143 (ptm160) REVERT: A 224 PHE cc_start: 0.8131 (m-80) cc_final: 0.6963 (p90) REVERT: A 229 PHE cc_start: 0.8202 (t80) cc_final: 0.7573 (t80) REVERT: A 243 MET cc_start: 0.8727 (mmm) cc_final: 0.8513 (mmm) REVERT: A 244 MET cc_start: 0.9415 (ttm) cc_final: 0.9168 (ttm) REVERT: A 303 ARG cc_start: 0.8789 (tpm170) cc_final: 0.8422 (tpm170) REVERT: A 346 LEU cc_start: 0.8961 (tp) cc_final: 0.8752 (tt) REVERT: A 948 LEU cc_start: 0.9101 (tp) cc_final: 0.8889 (tp) REVERT: A 961 MET cc_start: 0.8254 (tpp) cc_final: 0.7995 (tpp) outliers start: 50 outliers final: 35 residues processed: 167 average time/residue: 0.0740 time to fit residues: 19.1808 Evaluate side-chains 160 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 86 ILE 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 214 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 259 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 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 143 HIS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 262 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 110 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 40.0000 chunk 136 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082456 restraints weight = 30539.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083886 restraints weight = 15648.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084312 restraints weight = 10618.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084959 restraints weight = 10084.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084916 restraints weight = 8711.932| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9907 Z= 0.207 Angle : 0.616 10.849 13551 Z= 0.312 Chirality : 0.042 0.162 1657 Planarity : 0.003 0.046 1748 Dihedral : 4.439 49.356 1563 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 7.75 % Allowed : 23.39 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.23), residues: 1443 helix: 1.55 (0.18), residues: 880 sheet: -2.52 (0.55), residues: 75 loop : -1.07 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.012 0.001 TYR G 157 PHE 0.011 0.001 PHE G 258 TRP 0.010 0.001 TRP A 865 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9907) covalent geometry : angle 0.61553 (13551) hydrogen bonds : bond 0.05132 ( 640) hydrogen bonds : angle 4.20622 ( 1893) *********************** 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 180 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8505 (pp20) cc_final: 0.7770 (tp30) REVERT: A 54 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7713 (tm-30) REVERT: A 55 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8464 (ptm160) REVERT: A 212 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7734 (ttt) REVERT: A 224 PHE cc_start: 0.8258 (m-80) cc_final: 0.6980 (p90) REVERT: A 229 PHE cc_start: 0.8320 (t80) cc_final: 0.7722 (t80) REVERT: A 243 MET cc_start: 0.8832 (mmm) cc_final: 0.8625 (mmm) REVERT: A 244 MET cc_start: 0.9431 (ttm) cc_final: 0.9186 (ttm) REVERT: A 948 LEU cc_start: 0.9121 (tp) cc_final: 0.8846 (tp) REVERT: A 961 MET cc_start: 0.8372 (tpp) cc_final: 0.8103 (tpp) REVERT: A 983 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 1048 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8246 (tmm-80) REVERT: G 129 MET cc_start: 0.7847 (tmm) cc_final: 0.7339 (tmm) outliers start: 53 outliers final: 38 residues processed: 165 average time/residue: 0.0691 time to fit residues: 18.0252 Evaluate side-chains 164 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 86 ILE 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 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 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 1001 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1026 PHE 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 143 HIS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 262 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 268 ASN A 996 GLN G 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.108610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085017 restraints weight = 30360.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086670 restraints weight = 15255.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087570 restraints weight = 9990.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087824 restraints weight = 9330.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087970 restraints weight = 7971.747| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1919 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= 0.117 Angle : 0.563 11.662 13551 Z= 0.281 Chirality : 0.040 0.224 1657 Planarity : 0.003 0.042 1748 Dihedral : 4.240 48.123 1563 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.99 % Allowed : 24.85 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.23), residues: 1443 helix: 1.64 (0.18), residues: 888 sheet: -2.84 (0.53), residues: 77 loop : -0.97 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1048 TYR 0.010 0.001 TYR G 157 PHE 0.014 0.001 PHE A1107 TRP 0.007 0.001 TRP A 865 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9907) covalent geometry : angle 0.56336 (13551) hydrogen bonds : bond 0.04620 ( 640) hydrogen bonds : angle 3.95393 ( 1893) *********************** 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 171 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8395 (pp20) cc_final: 0.7621 (tp30) REVERT: A 54 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7593 (tm-30) REVERT: A 55 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8430 (ptm160) REVERT: A 212 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7676 (ttt) REVERT: A 224 PHE cc_start: 0.8197 (m-80) cc_final: 0.6914 (p90) REVERT: A 229 PHE cc_start: 0.8199 (t80) cc_final: 0.7542 (t80) REVERT: A 244 MET cc_start: 0.9386 (ttm) cc_final: 0.9123 (ttm) REVERT: A 303 ARG cc_start: 0.8750 (tpm170) cc_final: 0.8388 (tpm170) REVERT: A 948 LEU cc_start: 0.9104 (tp) cc_final: 0.8877 (tp) REVERT: A 961 MET cc_start: 0.8310 (tpp) cc_final: 0.8052 (tpp) REVERT: A 1048 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8233 (tmm-80) REVERT: G 129 MET cc_start: 0.7837 (tmm) cc_final: 0.7354 (tmm) outliers start: 41 outliers final: 32 residues processed: 157 average time/residue: 0.0684 time to fit residues: 16.5381 Evaluate side-chains 161 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 93 VAL 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 212 MET 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 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 845 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 1119 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 262 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 99 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 overall best weight: 2.3562 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.106257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082451 restraints weight = 30334.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083850 restraints weight = 15610.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083981 restraints weight = 10591.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085612 restraints weight = 10155.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085510 restraints weight = 8519.716| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9907 Z= 0.185 Angle : 0.622 11.013 13551 Z= 0.310 Chirality : 0.041 0.162 1657 Planarity : 0.003 0.046 1748 Dihedral : 4.372 47.724 1563 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.43 % Allowed : 24.56 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.23), residues: 1443 helix: 1.58 (0.18), residues: 885 sheet: -2.54 (0.54), residues: 75 loop : -1.04 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1048 TYR 0.011 0.001 TYR G 157 PHE 0.012 0.001 PHE A 931 TRP 0.008 0.001 TRP A 865 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9907) covalent geometry : angle 0.62153 (13551) hydrogen bonds : bond 0.05005 ( 640) hydrogen bonds : angle 4.13083 ( 1893) *********************** 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 171 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8471 (pp20) cc_final: 0.7722 (tp30) REVERT: A 54 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7676 (tm-30) REVERT: A 55 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8454 (ptm160) REVERT: A 212 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7684 (ttt) REVERT: A 224 PHE cc_start: 0.8265 (m-80) cc_final: 0.6976 (p90) REVERT: A 229 PHE cc_start: 0.8278 (t80) cc_final: 0.7662 (t80) REVERT: A 244 MET cc_start: 0.9411 (ttm) cc_final: 0.9113 (ttm) REVERT: A 948 LEU cc_start: 0.9130 (tp) cc_final: 0.8879 (tp) REVERT: A 983 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 1169 MET cc_start: 0.8064 (tpt) cc_final: 0.7608 (ttm) outliers start: 44 outliers final: 35 residues processed: 158 average time/residue: 0.0653 time to fit residues: 16.4173 Evaluate side-chains 161 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 86 ILE 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 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 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 845 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 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 152 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 262 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.104913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081267 restraints weight = 30641.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.082627 restraints weight = 15933.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083219 restraints weight = 10787.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083864 restraints weight = 10064.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083758 restraints weight = 8744.423| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9907 Z= 0.232 Angle : 0.679 14.957 13551 Z= 0.341 Chirality : 0.043 0.144 1657 Planarity : 0.004 0.051 1748 Dihedral : 4.686 49.542 1563 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.85 % Allowed : 25.29 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.23), residues: 1443 helix: 1.42 (0.18), residues: 879 sheet: -2.89 (0.57), residues: 67 loop : -1.10 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.013 0.001 TYR G 157 PHE 0.012 0.001 PHE G 258 TRP 0.012 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9907) covalent geometry : angle 0.67860 (13551) hydrogen bonds : bond 0.05457 ( 640) hydrogen bonds : angle 4.38876 ( 1893) ********************** 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 164 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8527 (pp20) cc_final: 0.7754 (tp30) REVERT: A 54 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7683 (tm-30) REVERT: A 55 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8531 (ptm160) REVERT: A 212 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7971 (ttt) REVERT: A 229 PHE cc_start: 0.8336 (t80) cc_final: 0.7747 (t80) REVERT: A 244 MET cc_start: 0.9434 (ttm) cc_final: 0.9144 (ttm) REVERT: A 320 LEU cc_start: 0.8662 (mp) cc_final: 0.8149 (tt) REVERT: A 948 LEU cc_start: 0.9147 (tp) cc_final: 0.8842 (tp) REVERT: A 983 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 1048 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8346 (tmm-80) outliers start: 40 outliers final: 32 residues processed: 155 average time/residue: 0.0589 time to fit residues: 14.5204 Evaluate side-chains 156 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 86 ILE 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 138 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 845 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 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 152 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 262 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.105305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081424 restraints weight = 30669.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082573 restraints weight = 16588.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083237 restraints weight = 11800.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083854 restraints weight = 10280.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083972 restraints weight = 8615.512| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9907 Z= 0.198 Angle : 0.667 14.089 13551 Z= 0.330 Chirality : 0.042 0.152 1657 Planarity : 0.003 0.051 1748 Dihedral : 4.649 50.111 1563 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.85 % Allowed : 25.73 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.23), residues: 1443 helix: 1.44 (0.18), residues: 875 sheet: -2.92 (0.56), residues: 67 loop : -1.14 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1048 TYR 0.014 0.001 TYR G 157 PHE 0.012 0.001 PHE A 931 TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9907) covalent geometry : angle 0.66683 (13551) hydrogen bonds : bond 0.05316 ( 640) hydrogen bonds : angle 4.32347 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1866.57 seconds wall clock time: 32 minutes 44.00 seconds (1964.00 seconds total)