Starting phenix.real_space_refine on Fri Jun 20 01:13:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxu_36713/06_2025/8jxu_36713_trim.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.046 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7296 2.51 5 N 1865 2.21 5 O 2040 1.98 5 H 11485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22749 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 22690 Classifications: {'peptide': 1410} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 42, 'TRANS': 1367} Chain breaks: 2 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.29, per 1000 atoms: 0.45 Number of scatterers: 22749 At special positions: 0 Unit cell: (88.81, 117.7, 155.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 57 16.00 P 5 15.00 Mg 1 11.99 O 2040 8.00 N 1865 7.00 C 7296 6.00 H 11485 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 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: 5.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 70.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.774A pdb=" N CYS A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 18 removed outlier: 3.776A pdb=" N LEU A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.513A pdb=" N GLN A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.790A pdb=" N LEU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.688A pdb=" N TYR A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 removed outlier: 3.850A pdb=" N LEU A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.726A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.663A pdb=" N TYR A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 129 through 157 removed outlier: 3.531A pdb=" N TRP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 4.740A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.612A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.641A pdb=" N ILE A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 262 removed outlier: 3.667A pdb=" N THR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 319 through 352 removed outlier: 3.704A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 356 through 393 removed outlier: 3.513A pdb=" N CYS A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 4.457A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.591A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 456 removed outlier: 4.162A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 3.838A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.026A pdb=" N ILE A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 517 through 551 removed outlier: 3.959A pdb=" N GLN A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.524A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.934A pdb=" N ALA A 576 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 589 through 618 Proline residue: A 597 - end of helix removed outlier: 3.516A pdb=" N SER A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 removed outlier: 3.502A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.813A pdb=" N GLN A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 4.131A pdb=" N MET A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.507A pdb=" N LEU A 751 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 removed outlier: 3.517A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 821 through 828 removed outlier: 4.336A pdb=" N PHE A 824 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 825 " --> pdb=" O MET A 822 " (cutoff:3.500A) Proline residue: A 826 - end of helix No H-bonds generated for 'chain 'A' and resid 821 through 828' Processing helix chain 'A' and resid 844 through 851 removed outlier: 3.956A pdb=" N LYS A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 863 removed outlier: 3.659A pdb=" N PHE A 862 " --> pdb=" O ASN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.986A pdb=" N TYR A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.512A pdb=" N PHE A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A1005 " --> pdb=" O SER A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 3.601A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1065 removed outlier: 4.016A pdb=" N VAL A1024 " --> pdb=" O ARG A1020 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.696A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 removed outlier: 3.920A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A1084 " --> pdb=" O ILE A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1120 removed outlier: 5.278A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Proline residue: A1096 - end of helix removed outlier: 3.550A pdb=" N ARG A1100 " --> pdb=" O PRO A1096 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1125 Processing helix chain 'A' and resid 1126 through 1146 removed outlier: 4.590A pdb=" N SER A1143 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR A1144 " --> pdb=" O PHE A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 removed outlier: 3.894A pdb=" N LEU A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1169 removed outlier: 3.786A pdb=" N TYR A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.595A pdb=" N LYS A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A1185 " --> pdb=" O ARG A1181 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A1229 " --> pdb=" O MET A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1266 removed outlier: 4.057A pdb=" N GLY A1239 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A1258 " --> pdb=" O TRP A1254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1276 removed outlier: 3.662A pdb=" N TYR A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.894A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1347 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1375 removed outlier: 4.663A pdb=" N ARG A1374 " --> pdb=" O HIS A1371 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU A1375 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1402 through 1413 removed outlier: 3.563A pdb=" N ILE A1406 " --> pdb=" O SER A1402 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 4.008A pdb=" N ALA A1450 " --> pdb=" O CYS A1446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1480 Processing helix chain 'A' and resid 1494 through 1498 removed outlier: 4.308A pdb=" N THR A1497 " --> pdb=" O ARG A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1536 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.720A pdb=" N HIS A 694 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL A 657 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG A 655 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.720A pdb=" N HIS A 694 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 689 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.268A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP A 785 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 704 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 782 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 818 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU A 784 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 7.014A pdb=" N ARG A1318 " --> pdb=" O GLN A1306 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN A1306 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A1320 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.570A pdb=" N THR A1378 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A1461 " --> pdb=" O THR A1378 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A1380 " --> pdb=" O ASP A1461 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A1330 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1507 " --> pdb=" O VAL A1333 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1839 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: 8.95 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11467 1.03 - 1.23: 31 1.23 - 1.42: 4720 1.42 - 1.62: 6676 1.62 - 1.81: 94 Bond restraints: 22988 Sorted by residual: bond pdb=" CA GLN A 383 " pdb=" C GLN A 383 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.38e-02 5.25e+03 1.29e+01 bond pdb=" CA ASN A1345 " pdb=" C ASN A1345 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.38e-02 5.25e+03 2.40e+00 bond pdb=" C4 ADP A1601 " pdb=" C5 ADP A1601 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C PHE A 382 " pdb=" N GLN A 383 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.38e-02 5.25e+03 1.58e+00 bond pdb=" CA ILE A 197 " pdb=" C ILE A 197 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.02e+00 ... (remaining 22983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.92: 41635 9.92 - 19.84: 0 19.84 - 29.77: 1 29.77 - 39.69: 0 39.69 - 49.61: 2 Bond angle restraints: 41638 Sorted by residual: angle pdb=" C ILE A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta sigma weight residual 119.92 140.93 -21.01 9.60e-01 1.09e+00 4.79e+02 angle pdb=" C ILE A 754 " pdb=" N GLY A 755 " pdb=" H GLY A 755 " ideal model delta sigma weight residual 125.19 75.58 49.61 3.00e+00 1.11e-01 2.73e+02 angle pdb=" CA GLY A 755 " pdb=" N GLY A 755 " pdb=" H GLY A 755 " ideal model delta sigma weight residual 114.89 65.35 49.54 3.00e+00 1.11e-01 2.73e+02 angle pdb=" CA MET A 988 " pdb=" CB MET A 988 " pdb=" CG MET A 988 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N VAL A 390 " pdb=" CA VAL A 390 " pdb=" C VAL A 390 " ideal model delta sigma weight residual 113.07 109.22 3.85 1.37e+00 5.33e-01 7.91e+00 ... (remaining 41633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 9720 19.65 - 39.30: 781 39.30 - 58.95: 218 58.95 - 78.60: 21 78.60 - 98.25: 7 Dihedral angle restraints: 10747 sinusoidal: 5845 harmonic: 4902 Sorted by residual: dihedral pdb=" O1B ADP A1601 " pdb=" O3A ADP A1601 " pdb=" PB ADP A1601 " pdb=" PA ADP A1601 " ideal model delta sinusoidal sigma weight residual -60.00 -158.25 98.25 1 2.00e+01 2.50e-03 2.74e+01 dihedral pdb=" C4' ADP A1601 " pdb=" C5' ADP A1601 " pdb=" O5' ADP A1601 " pdb=" PA ADP A1601 " ideal model delta sinusoidal sigma weight residual -180.00 -117.90 -62.10 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" CA GLU A 647 " pdb=" C GLU A 647 " pdb=" N HIS A 648 " pdb=" CA HIS A 648 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1614 0.058 - 0.115: 195 0.115 - 0.173: 12 0.173 - 0.230: 0 0.230 - 0.288: 3 Chirality restraints: 1824 Sorted by residual: chirality pdb=" C2' ATP A1602 " pdb=" C1' ATP A1602 " pdb=" C3' ATP A1602 " pdb=" O2' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ATP A1602 " pdb=" C2' ATP A1602 " pdb=" C4' ATP A1602 " pdb=" O3' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C4' ATP A1602 " pdb=" C3' ATP A1602 " pdb=" C5' ATP A1602 " pdb=" O4' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.49 -2.74 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1821 not shown) Planarity restraints: 3289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 596 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 597 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 474 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 475 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1383 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASP A1383 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A1383 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO A1384 " -0.009 2.00e-02 2.50e+03 ... (remaining 3286 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 648 2.13 - 2.75: 42517 2.75 - 3.37: 65426 3.37 - 3.98: 78941 3.98 - 4.60: 125978 Nonbonded interactions: 313510 Sorted by model distance: nonbonded pdb=" OE1 GLU A1352 " pdb=" H GLU A1352 " model vdw 1.513 2.450 nonbonded pdb=" OE1 GLU A 3 " pdb=" H GLU A 3 " model vdw 1.555 2.450 nonbonded pdb=" OE1 GLU A 504 " pdb=" H SER A1388 " model vdw 1.611 2.450 nonbonded pdb="HD21 ASN A 422 " pdb=" OD1 ASP A 496 " model vdw 1.612 2.450 nonbonded pdb=" OE1 GLU A1470 " pdb=" H GLU A1470 " model vdw 1.624 2.450 ... (remaining 313505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 43.030 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: 0.350 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 48.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.004 0.050 11504 Z= 0.172 Angle : 0.583 21.010 15606 Z= 0.348 Chirality : 0.038 0.288 1824 Planarity : 0.003 0.065 1924 Dihedral : 16.101 98.250 4202 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.24 % Allowed : 15.77 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1404 helix: -0.22 (0.18), residues: 850 sheet: -1.91 (0.59), residues: 67 loop : -1.14 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 999 HIS 0.002 0.001 HIS A1162 PHE 0.016 0.001 PHE A1530 TYR 0.014 0.001 TYR A 356 ARG 0.004 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.27211 ( 623) hydrogen bonds : angle 9.44029 ( 1839) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.26326 ( 2) covalent geometry : bond 0.00357 (11503) covalent geometry : angle 0.58258 (15604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 268 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.9418 (mt) cc_final: 0.9202 (mt) REVERT: A 378 LEU cc_start: 0.9256 (tp) cc_final: 0.9047 (tt) REVERT: A 978 SER cc_start: 0.9162 (m) cc_final: 0.8936 (p) REVERT: A 1069 MET cc_start: 0.7993 (mmm) cc_final: 0.7657 (mmm) outliers start: 3 outliers final: 3 residues processed: 269 average time/residue: 0.4366 time to fit residues: 183.8933 Evaluate side-chains 204 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 574 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 0.0030 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.051128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040732 restraints weight = 181509.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.042639 restraints weight = 76878.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044026 restraints weight = 44266.709| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11504 Z= 0.218 Angle : 0.690 8.983 15606 Z= 0.379 Chirality : 0.040 0.157 1824 Planarity : 0.004 0.055 1924 Dihedral : 6.854 89.099 1554 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 18.82 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1404 helix: -0.21 (0.17), residues: 890 sheet: -2.07 (0.60), residues: 66 loop : -1.07 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.006 0.001 HIS A1042 PHE 0.019 0.002 PHE A 977 TYR 0.019 0.001 TYR A 967 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.07661 ( 623) hydrogen bonds : angle 6.42033 ( 1839) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.36832 ( 2) covalent geometry : bond 0.00418 (11503) covalent geometry : angle 0.69019 (15604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9085 (mm-30) REVERT: A 328 LEU cc_start: 0.9667 (tp) cc_final: 0.9464 (tp) REVERT: A 419 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8779 (mt-10) REVERT: A 611 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9066 (tm-30) REVERT: A 822 MET cc_start: 0.9116 (mmp) cc_final: 0.8757 (mtp) REVERT: A 969 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8996 (tm-30) REVERT: A 988 MET cc_start: 0.9668 (tmm) cc_final: 0.9385 (tmm) REVERT: A 1069 MET cc_start: 0.9015 (mmm) cc_final: 0.8735 (tpp) REVERT: A 1103 ILE cc_start: 0.9635 (mt) cc_final: 0.9391 (tp) REVERT: A 1187 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 1270 GLU cc_start: 0.9497 (tm-30) cc_final: 0.9294 (tm-30) outliers start: 37 outliers final: 25 residues processed: 237 average time/residue: 0.4865 time to fit residues: 179.2274 Evaluate side-chains 219 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 5 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.041185 restraints weight = 179351.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.043138 restraints weight = 74515.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044508 restraints weight = 42380.059| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11504 Z= 0.146 Angle : 0.617 7.711 15606 Z= 0.323 Chirality : 0.039 0.160 1824 Planarity : 0.003 0.047 1924 Dihedral : 6.367 83.829 1552 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.72 % Allowed : 19.38 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1404 helix: 0.12 (0.17), residues: 887 sheet: -2.08 (0.56), residues: 76 loop : -1.03 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.003 0.001 HIS A 439 PHE 0.018 0.001 PHE A1037 TYR 0.007 0.001 TYR A 319 ARG 0.004 0.000 ARG A1083 Details of bonding type rmsd hydrogen bonds : bond 0.06277 ( 623) hydrogen bonds : angle 5.60190 ( 1839) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.33420 ( 2) covalent geometry : bond 0.00290 (11503) covalent geometry : angle 0.61679 (15604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.9838 (OUTLIER) cc_final: 0.9604 (tt0) REVERT: A 172 TYR cc_start: 0.9455 (t80) cc_final: 0.9040 (t80) REVERT: A 243 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 249 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9059 (mm-30) REVERT: A 328 LEU cc_start: 0.9615 (tp) cc_final: 0.9387 (tp) REVERT: A 419 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8695 (mt-10) REVERT: A 422 ASN cc_start: 0.9792 (t0) cc_final: 0.9559 (t0) REVERT: A 599 MET cc_start: 0.9599 (tmm) cc_final: 0.9349 (tmm) REVERT: A 611 GLU cc_start: 0.9460 (tm-30) cc_final: 0.9000 (tm-30) REVERT: A 757 LYS cc_start: 0.9741 (ttmm) cc_final: 0.9198 (tptp) REVERT: A 822 MET cc_start: 0.9085 (mmp) cc_final: 0.8707 (mtp) REVERT: A 969 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8997 (tm-30) REVERT: A 988 MET cc_start: 0.9670 (tmm) cc_final: 0.9444 (tmm) REVERT: A 1069 MET cc_start: 0.9033 (mmm) cc_final: 0.8558 (mmm) REVERT: A 1090 THR cc_start: 0.9782 (OUTLIER) cc_final: 0.9554 (p) REVERT: A 1103 ILE cc_start: 0.9535 (mt) cc_final: 0.9273 (tp) REVERT: A 1194 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8988 (mt0) REVERT: A 1261 GLU cc_start: 0.9463 (tp30) cc_final: 0.9257 (tp30) REVERT: A 1458 LEU cc_start: 0.9799 (tt) cc_final: 0.9252 (mt) outliers start: 34 outliers final: 22 residues processed: 223 average time/residue: 0.4035 time to fit residues: 140.9911 Evaluate side-chains 212 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 36 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 43 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042079 restraints weight = 183712.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044027 restraints weight = 77616.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045424 restraints weight = 44608.773| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11504 Z= 0.153 Angle : 0.595 6.636 15606 Z= 0.315 Chirality : 0.038 0.149 1824 Planarity : 0.003 0.043 1924 Dihedral : 6.205 84.104 1552 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.48 % Allowed : 21.54 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1404 helix: 0.41 (0.17), residues: 888 sheet: -1.93 (0.57), residues: 76 loop : -0.95 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.003 0.001 HIS A1371 PHE 0.018 0.001 PHE A1037 TYR 0.012 0.001 TYR A 967 ARG 0.003 0.000 ARG A1083 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 623) hydrogen bonds : angle 5.34847 ( 1839) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.33549 ( 2) covalent geometry : bond 0.00305 (11503) covalent geometry : angle 0.59483 (15604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9722 (mp) cc_final: 0.9496 (mm) REVERT: A 243 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8942 (tm-30) REVERT: A 249 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9049 (mm-30) REVERT: A 327 LEU cc_start: 0.9691 (mt) cc_final: 0.9448 (tp) REVERT: A 419 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 440 MET cc_start: 0.9492 (mmm) cc_final: 0.9259 (mmp) REVERT: A 496 ASP cc_start: 0.8987 (m-30) cc_final: 0.8658 (m-30) REVERT: A 599 MET cc_start: 0.9573 (tmm) cc_final: 0.9323 (tmm) REVERT: A 611 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9000 (tm-30) REVERT: A 687 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8778 (mp0) REVERT: A 822 MET cc_start: 0.9082 (mmp) cc_final: 0.8708 (mtp) REVERT: A 969 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9136 (tm-30) REVERT: A 1069 MET cc_start: 0.9041 (mmm) cc_final: 0.8627 (mmm) REVERT: A 1097 GLN cc_start: 0.9512 (tm-30) cc_final: 0.9299 (tm-30) REVERT: A 1103 ILE cc_start: 0.9571 (mt) cc_final: 0.9310 (tp) REVERT: A 1202 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9190 (p) REVERT: A 1226 MET cc_start: 0.9189 (mmp) cc_final: 0.8944 (mmp) REVERT: A 1458 LEU cc_start: 0.9801 (tt) cc_final: 0.9269 (mt) outliers start: 31 outliers final: 20 residues processed: 213 average time/residue: 0.4073 time to fit residues: 135.8836 Evaluate side-chains 198 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 0.0000 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042278 restraints weight = 179591.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044281 restraints weight = 77452.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045668 restraints weight = 44440.613| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11504 Z= 0.119 Angle : 0.586 6.859 15606 Z= 0.299 Chirality : 0.038 0.150 1824 Planarity : 0.003 0.043 1924 Dihedral : 6.170 88.239 1552 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.40 % Allowed : 22.10 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1404 helix: 0.66 (0.17), residues: 889 sheet: -1.75 (0.58), residues: 76 loop : -0.90 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 709 HIS 0.003 0.001 HIS A 439 PHE 0.012 0.001 PHE A 5 TYR 0.007 0.001 TYR A 319 ARG 0.003 0.000 ARG A1083 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 623) hydrogen bonds : angle 5.01194 ( 1839) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.32167 ( 2) covalent geometry : bond 0.00247 (11503) covalent geometry : angle 0.58596 (15604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9710 (mp) cc_final: 0.9474 (mm) REVERT: A 118 GLN cc_start: 0.9830 (OUTLIER) cc_final: 0.9570 (tt0) REVERT: A 243 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8972 (tm-30) REVERT: A 419 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 440 MET cc_start: 0.9506 (mmm) cc_final: 0.9156 (mmm) REVERT: A 496 ASP cc_start: 0.8865 (m-30) cc_final: 0.8625 (m-30) REVERT: A 599 MET cc_start: 0.9583 (tmm) cc_final: 0.9295 (tmm) REVERT: A 611 GLU cc_start: 0.9440 (tm-30) cc_final: 0.8983 (tm-30) REVERT: A 822 MET cc_start: 0.9131 (mmp) cc_final: 0.8755 (mtp) REVERT: A 969 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9110 (tm-30) REVERT: A 1069 MET cc_start: 0.9029 (mmm) cc_final: 0.8622 (mmm) REVERT: A 1103 ILE cc_start: 0.9539 (mt) cc_final: 0.9270 (tp) REVERT: A 1392 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.8782 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9791 (tt) cc_final: 0.9284 (mt) outliers start: 30 outliers final: 24 residues processed: 211 average time/residue: 0.4236 time to fit residues: 138.6824 Evaluate side-chains 208 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 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 = 0.3189 r_free = 0.3189 target = 0.052663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041845 restraints weight = 181118.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043826 restraints weight = 79697.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045247 restraints weight = 46304.363| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11504 Z= 0.124 Angle : 0.585 7.275 15606 Z= 0.299 Chirality : 0.038 0.145 1824 Planarity : 0.003 0.042 1924 Dihedral : 6.122 87.842 1552 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 22.42 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1404 helix: 0.83 (0.17), residues: 890 sheet: -1.76 (0.58), residues: 76 loop : -0.84 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.003 0.001 HIS A 439 PHE 0.011 0.001 PHE A 437 TYR 0.007 0.001 TYR A 217 ARG 0.002 0.000 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 623) hydrogen bonds : angle 4.88602 ( 1839) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.15039 ( 2) covalent geometry : bond 0.00264 (11503) covalent geometry : angle 0.58464 (15604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9719 (mp) cc_final: 0.9470 (mm) REVERT: A 118 GLN cc_start: 0.9823 (OUTLIER) cc_final: 0.9574 (tt0) REVERT: A 243 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8939 (tm-30) REVERT: A 419 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 440 MET cc_start: 0.9513 (mmm) cc_final: 0.9171 (mmm) REVERT: A 496 ASP cc_start: 0.8807 (m-30) cc_final: 0.8551 (m-30) REVERT: A 599 MET cc_start: 0.9578 (tmm) cc_final: 0.9282 (tmm) REVERT: A 611 GLU cc_start: 0.9430 (tm-30) cc_final: 0.8979 (tm-30) REVERT: A 687 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8761 (mp0) REVERT: A 822 MET cc_start: 0.9106 (mmp) cc_final: 0.8751 (mtp) REVERT: A 969 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9123 (tm-30) REVERT: A 1069 MET cc_start: 0.9021 (mmm) cc_final: 0.8623 (mmm) REVERT: A 1103 ILE cc_start: 0.9557 (mt) cc_final: 0.9290 (tp) REVERT: A 1118 MET cc_start: 0.9172 (mmm) cc_final: 0.8941 (mmm) REVERT: A 1458 LEU cc_start: 0.9785 (tt) cc_final: 0.9287 (mt) outliers start: 28 outliers final: 25 residues processed: 200 average time/residue: 0.4156 time to fit residues: 131.0802 Evaluate side-chains 210 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 66 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042182 restraints weight = 184784.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044101 restraints weight = 78968.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045454 restraints weight = 45499.194| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11504 Z= 0.162 Angle : 0.581 7.141 15606 Z= 0.304 Chirality : 0.037 0.151 1824 Planarity : 0.003 0.044 1924 Dihedral : 6.055 85.329 1552 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.40 % Allowed : 22.66 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1404 helix: 0.96 (0.17), residues: 893 sheet: -1.82 (0.58), residues: 76 loop : -0.87 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 709 HIS 0.003 0.001 HIS A 439 PHE 0.012 0.001 PHE A 437 TYR 0.008 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 623) hydrogen bonds : angle 4.95858 ( 1839) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.09164 ( 2) covalent geometry : bond 0.00319 (11503) covalent geometry : angle 0.58140 (15604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9730 (mp) cc_final: 0.9491 (mm) REVERT: A 118 GLN cc_start: 0.9822 (OUTLIER) cc_final: 0.9511 (tt0) REVERT: A 243 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8950 (tm-30) REVERT: A 249 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9055 (mm-30) REVERT: A 419 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 440 MET cc_start: 0.9522 (mmm) cc_final: 0.9199 (mmm) REVERT: A 598 MET cc_start: 0.9327 (ppp) cc_final: 0.9121 (ppp) REVERT: A 599 MET cc_start: 0.9588 (tmm) cc_final: 0.9331 (tmm) REVERT: A 611 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9011 (tm-30) REVERT: A 687 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8752 (mp0) REVERT: A 822 MET cc_start: 0.9119 (mmp) cc_final: 0.8792 (mtp) REVERT: A 969 GLU cc_start: 0.9442 (tm-30) cc_final: 0.9204 (tm-30) REVERT: A 1069 MET cc_start: 0.9034 (mmm) cc_final: 0.8284 (tpp) REVERT: A 1103 ILE cc_start: 0.9554 (mt) cc_final: 0.9291 (tp) REVERT: A 1118 MET cc_start: 0.9231 (mmm) cc_final: 0.8999 (mmm) REVERT: A 1383 ASP cc_start: 0.9528 (p0) cc_final: 0.9309 (p0) REVERT: A 1392 ARG cc_start: 0.9607 (OUTLIER) cc_final: 0.8816 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9786 (tt) cc_final: 0.9301 (mt) outliers start: 30 outliers final: 23 residues processed: 199 average time/residue: 0.4415 time to fit residues: 134.9640 Evaluate side-chains 200 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041499 restraints weight = 190348.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.043332 restraints weight = 81838.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044647 restraints weight = 47302.678| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11504 Z= 0.270 Angle : 0.628 7.429 15606 Z= 0.341 Chirality : 0.038 0.135 1824 Planarity : 0.003 0.048 1924 Dihedral : 6.127 84.794 1552 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.48 % Allowed : 23.06 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1404 helix: 0.81 (0.17), residues: 893 sheet: -1.93 (0.58), residues: 76 loop : -0.98 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.004 0.001 HIS A1371 PHE 0.016 0.001 PHE A 135 TYR 0.008 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 623) hydrogen bonds : angle 5.28309 ( 1839) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.17492 ( 2) covalent geometry : bond 0.00513 (11503) covalent geometry : angle 0.62790 (15604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9756 (mp) cc_final: 0.9527 (mm) REVERT: A 243 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8950 (tm-30) REVERT: A 327 LEU cc_start: 0.9715 (mt) cc_final: 0.9485 (tp) REVERT: A 419 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 440 MET cc_start: 0.9526 (mmm) cc_final: 0.9234 (mmm) REVERT: A 599 MET cc_start: 0.9590 (tmm) cc_final: 0.9282 (tmm) REVERT: A 611 GLU cc_start: 0.9467 (tm-30) cc_final: 0.9035 (tm-30) REVERT: A 822 MET cc_start: 0.9017 (mmp) cc_final: 0.8757 (mtp) REVERT: A 969 GLU cc_start: 0.9475 (tm-30) cc_final: 0.9235 (tm-30) REVERT: A 1069 MET cc_start: 0.9048 (mmm) cc_final: 0.8328 (tpp) REVERT: A 1103 ILE cc_start: 0.9587 (mt) cc_final: 0.9324 (tp) REVERT: A 1118 MET cc_start: 0.9246 (mmm) cc_final: 0.9016 (mmm) REVERT: A 1202 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9185 (p) REVERT: A 1392 ARG cc_start: 0.9625 (OUTLIER) cc_final: 0.8823 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9787 (tt) cc_final: 0.9315 (mt) outliers start: 31 outliers final: 26 residues processed: 188 average time/residue: 0.4481 time to fit residues: 132.0185 Evaluate side-chains 193 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 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 = 0.3185 r_free = 0.3185 target = 0.052076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.041399 restraints weight = 184027.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043347 restraints weight = 80804.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044734 restraints weight = 46884.650| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11504 Z= 0.119 Angle : 0.604 8.022 15606 Z= 0.304 Chirality : 0.038 0.145 1824 Planarity : 0.004 0.066 1924 Dihedral : 6.156 89.909 1552 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 23.38 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1404 helix: 1.22 (0.17), residues: 893 sheet: -1.87 (0.58), residues: 76 loop : -0.83 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.003 0.001 HIS A 439 PHE 0.010 0.001 PHE A 382 TYR 0.009 0.001 TYR A 967 ARG 0.009 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 623) hydrogen bonds : angle 4.76554 ( 1839) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.28772 ( 2) covalent geometry : bond 0.00254 (11503) covalent geometry : angle 0.60430 (15604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9040 (mm-30) REVERT: A 419 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 440 MET cc_start: 0.9522 (mmm) cc_final: 0.9255 (mmm) REVERT: A 598 MET cc_start: 0.9317 (ppp) cc_final: 0.9106 (ppp) REVERT: A 599 MET cc_start: 0.9585 (tmm) cc_final: 0.9322 (tmm) REVERT: A 611 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9017 (tm-30) REVERT: A 687 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8739 (mp0) REVERT: A 822 MET cc_start: 0.9117 (mmp) cc_final: 0.8774 (mtp) REVERT: A 969 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9206 (tm-30) REVERT: A 1103 ILE cc_start: 0.9550 (mt) cc_final: 0.9273 (tp) REVERT: A 1116 ILE cc_start: 0.9520 (mt) cc_final: 0.9282 (tp) REVERT: A 1118 MET cc_start: 0.9237 (mmm) cc_final: 0.9004 (mmm) REVERT: A 1392 ARG cc_start: 0.9614 (OUTLIER) cc_final: 0.8799 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9770 (tt) cc_final: 0.9297 (mt) outliers start: 27 outliers final: 25 residues processed: 199 average time/residue: 0.4407 time to fit residues: 136.1691 Evaluate side-chains 197 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041378 restraints weight = 187074.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043268 restraints weight = 80113.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.044612 restraints weight = 46126.850| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11504 Z= 0.186 Angle : 0.608 7.582 15606 Z= 0.319 Chirality : 0.038 0.140 1824 Planarity : 0.003 0.047 1924 Dihedral : 6.118 86.701 1552 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.16 % Allowed : 23.54 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1404 helix: 1.24 (0.17), residues: 889 sheet: -1.83 (0.59), residues: 76 loop : -0.86 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.004 0.001 HIS A 439 PHE 0.028 0.001 PHE A 437 TYR 0.010 0.001 TYR A 217 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 623) hydrogen bonds : angle 4.96560 ( 1839) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.06920 ( 2) covalent geometry : bond 0.00365 (11503) covalent geometry : angle 0.60783 (15604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8660 (mt-10) REVERT: A 440 MET cc_start: 0.9531 (mmm) cc_final: 0.9281 (mmm) REVERT: A 599 MET cc_start: 0.9602 (tmm) cc_final: 0.9288 (tmm) REVERT: A 611 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9026 (tm-30) REVERT: A 687 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8773 (mp0) REVERT: A 756 GLU cc_start: 0.8899 (pt0) cc_final: 0.8664 (pm20) REVERT: A 822 MET cc_start: 0.9024 (mmp) cc_final: 0.8764 (mtp) REVERT: A 969 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9250 (tm-30) REVERT: A 1069 MET cc_start: 0.9056 (mmm) cc_final: 0.8332 (tpp) REVERT: A 1103 ILE cc_start: 0.9578 (mt) cc_final: 0.9305 (tp) REVERT: A 1116 ILE cc_start: 0.9547 (mt) cc_final: 0.9320 (tp) REVERT: A 1392 ARG cc_start: 0.9623 (OUTLIER) cc_final: 0.8821 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9777 (tt) cc_final: 0.9310 (mt) outliers start: 27 outliers final: 25 residues processed: 187 average time/residue: 0.4203 time to fit residues: 122.4407 Evaluate side-chains 194 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1194 GLN Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.051699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041264 restraints weight = 189180.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.043116 restraints weight = 81832.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044478 restraints weight = 47218.827| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11504 Z= 0.229 Angle : 0.632 7.467 15606 Z= 0.336 Chirality : 0.038 0.136 1824 Planarity : 0.004 0.048 1924 Dihedral : 6.158 87.200 1552 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.16 % Allowed : 23.54 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1404 helix: 1.12 (0.17), residues: 891 sheet: -1.83 (0.59), residues: 76 loop : -0.93 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 309 HIS 0.004 0.001 HIS A 439 PHE 0.033 0.001 PHE A1037 TYR 0.009 0.001 TYR A 217 ARG 0.003 0.000 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 623) hydrogen bonds : angle 5.12946 ( 1839) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.09580 ( 2) covalent geometry : bond 0.00438 (11503) covalent geometry : angle 0.63169 (15604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.17 seconds wall clock time: 119 minutes 56.14 seconds (7196.14 seconds total)