Starting phenix.real_space_refine on Sun Oct 12 09:27:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxu_36713/10_2025/8jxu_36713_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxu_36713/10_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_36713/10_2025/8jxu_36713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxu_36713/10_2025/8jxu_36713.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxu_36713/10_2025/8jxu_36713_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxu_36713/10_2025/8jxu_36713_trim.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.84, per 1000 atoms: 0.17 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: 2.07 Conformation dependent library (CDL) restraints added in 528.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 5.56 Time building geometry restraints manager: 2.76 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: 0.910 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- 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 : 7.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG A 590 TYR 0.014 0.001 TYR A 356 PHE 0.016 0.001 PHE A1530 TRP 0.009 0.001 TRP A 999 HIS 0.002 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00357 (11503) covalent geometry : angle 0.58258 (15604) SS BOND : bond 0.00165 ( 1) SS BOND : angle 0.26326 ( 2) hydrogen bonds : bond 0.27211 ( 623) hydrogen bonds : angle 9.44029 ( 1839) *********************** 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 : 0.623 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: 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: 0.1928 time to fit residues: 81.2511 Evaluate side-chains 203 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 159 ASN A1193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.052005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041575 restraints weight = 178951.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043558 restraints weight = 76278.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.044917 restraints weight = 43606.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045960 restraints weight = 29377.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046488 restraints weight = 21394.541| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2244 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= 0.170 Angle : 0.687 9.423 15606 Z= 0.366 Chirality : 0.040 0.168 1824 Planarity : 0.004 0.053 1924 Dihedral : 6.822 87.362 1554 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.88 % Allowed : 18.49 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.22), residues: 1404 helix: -0.12 (0.17), residues: 884 sheet: -2.02 (0.60), residues: 66 loop : -1.08 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.021 0.001 TYR A 967 PHE 0.019 0.002 PHE A 977 TRP 0.009 0.001 TRP A 358 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00327 (11503) covalent geometry : angle 0.68678 (15604) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.36859 ( 2) hydrogen bonds : bond 0.07677 ( 623) hydrogen bonds : angle 6.22485 ( 1839) *********************** 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 258 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.825 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 118 GLN cc_start: 0.9815 (OUTLIER) cc_final: 0.9592 (tt0) REVERT: A 328 LEU cc_start: 0.9638 (tp) cc_final: 0.9423 (tp) REVERT: A 419 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8774 (mt-10) REVERT: A 501 ILE cc_start: 0.9840 (tp) cc_final: 0.9635 (tp) REVERT: A 611 GLU cc_start: 0.9453 (tm-30) cc_final: 0.9018 (tm-30) REVERT: A 616 TYR cc_start: 0.9554 (t80) cc_final: 0.9100 (t80) REVERT: A 822 MET cc_start: 0.9096 (mmp) cc_final: 0.8739 (mtp) REVERT: A 988 MET cc_start: 0.9648 (tmm) cc_final: 0.9395 (tmm) REVERT: A 1069 MET cc_start: 0.8986 (mmm) cc_final: 0.8704 (tpp) REVERT: A 1103 ILE cc_start: 0.9603 (mt) cc_final: 0.9354 (tp) REVERT: A 1115 MET cc_start: 0.8950 (mmm) cc_final: 0.8740 (mmm) REVERT: A 1187 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8715 (tm-30) REVERT: A 1393 MET cc_start: 0.9214 (ptp) cc_final: 0.8976 (ptm) outliers start: 36 outliers final: 20 residues processed: 243 average time/residue: 0.1880 time to fit residues: 71.2583 Evaluate side-chains 221 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 431 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 553 THR 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 1194 GLN Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 138 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.051435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.040912 restraints weight = 180813.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042855 restraints weight = 76077.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044245 restraints weight = 43508.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.045209 restraints weight = 29161.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.045836 restraints weight = 21504.956| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11504 Z= 0.168 Angle : 0.612 6.951 15606 Z= 0.327 Chirality : 0.038 0.156 1824 Planarity : 0.004 0.044 1924 Dihedral : 6.398 83.694 1552 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.00 % Allowed : 20.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1404 helix: 0.10 (0.17), residues: 882 sheet: -2.11 (0.55), residues: 76 loop : -0.99 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.007 0.001 TYR A 217 PHE 0.022 0.001 PHE A 550 TRP 0.013 0.001 TRP A 709 HIS 0.003 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00332 (11503) covalent geometry : angle 0.61232 (15604) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.39512 ( 2) hydrogen bonds : bond 0.06320 ( 623) hydrogen bonds : angle 5.69188 ( 1839) *********************** 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 229 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.656 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9716 (mp) cc_final: 0.9504 (mm) REVERT: A 118 GLN cc_start: 0.9841 (OUTLIER) cc_final: 0.9599 (tt0) REVERT: A 172 TYR cc_start: 0.9441 (t80) cc_final: 0.9054 (t80) REVERT: A 249 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9029 (mm-30) REVERT: A 328 LEU cc_start: 0.9624 (tp) cc_final: 0.9381 (tp) REVERT: A 419 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 422 ASN cc_start: 0.9798 (t0) cc_final: 0.9572 (t0) REVERT: A 611 GLU cc_start: 0.9438 (tm-30) cc_final: 0.8992 (tm-30) REVERT: A 616 TYR cc_start: 0.9595 (t80) cc_final: 0.9182 (t80) REVERT: A 617 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9362 (mm) REVERT: A 757 LYS cc_start: 0.9765 (mtpp) cc_final: 0.9373 (tptp) REVERT: A 822 MET cc_start: 0.9025 (mmp) cc_final: 0.8685 (mtp) REVERT: A 1069 MET cc_start: 0.9014 (mmm) cc_final: 0.8563 (mmm) REVERT: A 1103 ILE cc_start: 0.9541 (mt) cc_final: 0.9289 (tp) REVERT: A 1451 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9440 (mt) REVERT: A 1458 LEU cc_start: 0.9800 (tt) cc_final: 0.9283 (mt) outliers start: 25 outliers final: 17 residues processed: 220 average time/residue: 0.2064 time to fit residues: 70.8156 Evaluate side-chains 206 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 118 GLN 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 451 SER Chi-restraints excluded: chain A residue 455 LEU 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 617 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1173 ILE 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 118 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 0.0670 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1304 ASN A1394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.053333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042386 restraints weight = 187565.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044323 restraints weight = 78998.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045667 restraints weight = 45253.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046644 restraints weight = 30635.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047360 restraints weight = 22911.171| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11504 Z= 0.200 Angle : 0.618 7.051 15606 Z= 0.329 Chirality : 0.038 0.197 1824 Planarity : 0.003 0.042 1924 Dihedral : 6.213 80.741 1552 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.56 % Allowed : 21.38 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1404 helix: 0.24 (0.17), residues: 893 sheet: -2.01 (0.56), residues: 76 loop : -1.04 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.013 0.001 TYR A 967 PHE 0.018 0.001 PHE A 437 TRP 0.007 0.001 TRP A 309 HIS 0.004 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00383 (11503) covalent geometry : angle 0.61820 (15604) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.43289 ( 2) hydrogen bonds : bond 0.05400 ( 623) hydrogen bonds : angle 5.46666 ( 1839) *********************** 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 225 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.650 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: A 75 LEU cc_start: 0.9725 (mp) cc_final: 0.9501 (mm) REVERT: A 172 TYR cc_start: 0.9525 (t80) cc_final: 0.9257 (t80) REVERT: A 243 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 246 MET cc_start: 0.9207 (tmm) cc_final: 0.8920 (tmm) REVERT: A 249 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9033 (mm-30) REVERT: A 328 LEU cc_start: 0.9598 (tp) cc_final: 0.9365 (tp) REVERT: A 419 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8691 (mt-10) REVERT: A 496 ASP cc_start: 0.9060 (m-30) cc_final: 0.8705 (m-30) REVERT: A 599 MET cc_start: 0.9613 (tmm) cc_final: 0.9412 (tmm) REVERT: A 611 GLU cc_start: 0.9429 (tm-30) cc_final: 0.8977 (tm-30) REVERT: A 616 TYR cc_start: 0.9671 (t80) cc_final: 0.9348 (t80) REVERT: A 687 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8732 (mp0) REVERT: A 757 LYS cc_start: 0.9759 (mtpp) cc_final: 0.9530 (mtmm) REVERT: A 822 MET cc_start: 0.9060 (mmp) cc_final: 0.8751 (mtp) REVERT: A 1069 MET cc_start: 0.9019 (mmm) cc_final: 0.8219 (tpp) REVERT: A 1097 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9299 (tm-30) REVERT: A 1103 ILE cc_start: 0.9577 (mt) cc_final: 0.9323 (tp) REVERT: A 1202 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9181 (p) REVERT: A 1458 LEU cc_start: 0.9808 (tt) cc_final: 0.9294 (mt) outliers start: 32 outliers final: 23 residues processed: 215 average time/residue: 0.2046 time to fit residues: 68.2717 Evaluate side-chains 202 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 66 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 171 SER 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 455 LEU 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 971 LEU 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 1202 THR Chi-restraints excluded: chain A residue 1445 LEU 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 54 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.053422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.042588 restraints weight = 180929.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.044507 restraints weight = 75379.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.045879 restraints weight = 43033.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.046858 restraints weight = 28879.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.047554 restraints weight = 21304.411| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.003 0.032 11504 Z= 0.147 Angle : 0.583 6.783 15606 Z= 0.307 Chirality : 0.038 0.167 1824 Planarity : 0.003 0.039 1924 Dihedral : 6.204 87.141 1552 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.56 % Allowed : 21.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1404 helix: 0.54 (0.17), residues: 888 sheet: -1.90 (0.57), residues: 76 loop : -0.98 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1271 TYR 0.007 0.001 TYR A 319 PHE 0.014 0.001 PHE A 135 TRP 0.008 0.001 TRP A 309 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00294 (11503) covalent geometry : angle 0.58309 (15604) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.32730 ( 2) hydrogen bonds : bond 0.05030 ( 623) hydrogen bonds : angle 5.17730 ( 1839) *********************** 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 226 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.632 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: 0.9720 (mp) cc_final: 0.9496 (mm) REVERT: A 172 TYR cc_start: 0.9493 (t80) cc_final: 0.9275 (t80) REVERT: A 243 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8609 (tm-30) REVERT: A 246 MET cc_start: 0.9208 (tmm) cc_final: 0.8844 (tmm) REVERT: A 249 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8992 (mm-30) REVERT: A 328 LEU cc_start: 0.9613 (tp) cc_final: 0.9381 (tp) REVERT: A 419 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 496 ASP cc_start: 0.9012 (m-30) cc_final: 0.8687 (m-30) REVERT: A 598 MET cc_start: 0.9296 (ppp) cc_final: 0.9061 (ppp) REVERT: A 611 GLU cc_start: 0.9408 (tm-30) cc_final: 0.8937 (tm-30) REVERT: A 616 TYR cc_start: 0.9670 (t80) cc_final: 0.9362 (t80) REVERT: A 687 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8736 (mp0) REVERT: A 757 LYS cc_start: 0.9743 (mtpp) cc_final: 0.9540 (mtmm) REVERT: A 822 MET cc_start: 0.9047 (mmp) cc_final: 0.8739 (mtp) REVERT: A 1069 MET cc_start: 0.9005 (mmm) cc_final: 0.8208 (tpp) REVERT: A 1097 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9270 (tm-30) REVERT: A 1103 ILE cc_start: 0.9574 (mt) cc_final: 0.9313 (tp) REVERT: A 1202 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9152 (p) REVERT: A 1226 MET cc_start: 0.9505 (tpp) cc_final: 0.9200 (mmp) REVERT: A 1392 ARG cc_start: 0.9619 (OUTLIER) cc_final: 0.8836 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9792 (tt) cc_final: 0.9303 (mt) outliers start: 32 outliers final: 25 residues processed: 216 average time/residue: 0.2070 time to fit residues: 68.9615 Evaluate side-chains 208 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 66 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 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 382 PHE 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 553 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 1000 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 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 30 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** 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 = 0.3192 r_free = 0.3192 target = 0.052070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041383 restraints weight = 187718.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043262 restraints weight = 79992.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044628 restraints weight = 46306.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.045553 restraints weight = 31213.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046229 restraints weight = 23480.633| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3744 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= 0.179 Angle : 0.596 6.817 15606 Z= 0.315 Chirality : 0.038 0.143 1824 Planarity : 0.003 0.040 1924 Dihedral : 6.168 85.863 1552 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.56 % Allowed : 22.66 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1404 helix: 0.68 (0.17), residues: 891 sheet: -1.87 (0.57), residues: 76 loop : -0.94 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1271 TYR 0.008 0.001 TYR A 217 PHE 0.014 0.001 PHE A 437 TRP 0.007 0.001 TRP A 309 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00349 (11503) covalent geometry : angle 0.59556 (15604) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.17162 ( 2) hydrogen bonds : bond 0.04775 ( 623) hydrogen bonds : angle 5.20398 ( 1839) *********************** 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 219 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.537 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: A 75 LEU cc_start: 0.9727 (mp) cc_final: 0.9501 (mm) REVERT: A 172 TYR cc_start: 0.9531 (t80) cc_final: 0.9310 (t80) REVERT: A 243 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 246 MET cc_start: 0.9238 (tmm) cc_final: 0.8861 (tmm) REVERT: A 249 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9011 (mm-30) REVERT: A 328 LEU cc_start: 0.9607 (tp) cc_final: 0.9396 (tp) REVERT: A 419 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 496 ASP cc_start: 0.9058 (m-30) cc_final: 0.8690 (m-30) REVERT: A 598 MET cc_start: 0.9285 (ppp) cc_final: 0.9046 (ppp) REVERT: A 611 GLU cc_start: 0.9438 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 616 TYR cc_start: 0.9706 (t80) cc_final: 0.9430 (t80) REVERT: A 687 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8742 (mp0) REVERT: A 757 LYS cc_start: 0.9753 (mtpp) cc_final: 0.9548 (mtmm) REVERT: A 822 MET cc_start: 0.9075 (mmp) cc_final: 0.8761 (mtp) REVERT: A 988 MET cc_start: 0.9655 (ppp) cc_final: 0.9242 (ppp) REVERT: A 1069 MET cc_start: 0.9011 (mmm) cc_final: 0.8242 (tpp) REVERT: A 1097 GLN cc_start: 0.9487 (tm-30) cc_final: 0.9279 (tm-30) REVERT: A 1103 ILE cc_start: 0.9557 (mt) cc_final: 0.9287 (tp) REVERT: A 1202 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9148 (p) REVERT: A 1226 MET cc_start: 0.9540 (tpp) cc_final: 0.9234 (mmp) REVERT: A 1261 GLU cc_start: 0.9437 (tp30) cc_final: 0.9125 (tm-30) REVERT: A 1392 ARG cc_start: 0.9629 (OUTLIER) cc_final: 0.8814 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9793 (tt) cc_final: 0.9315 (mt) outliers start: 32 outliers final: 28 residues processed: 209 average time/residue: 0.2158 time to fit residues: 68.6778 Evaluate side-chains 207 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 66 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 358 TRP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU 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 617 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 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 1392 ARG 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 70 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041975 restraints weight = 188051.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043841 restraints weight = 79826.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045181 restraints weight = 45824.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.046118 restraints weight = 30826.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046772 restraints weight = 22936.214| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11504 Z= 0.208 Angle : 0.603 7.511 15606 Z= 0.321 Chirality : 0.038 0.141 1824 Planarity : 0.003 0.040 1924 Dihedral : 6.199 86.747 1552 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.32 % Allowed : 23.78 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.22), residues: 1404 helix: 0.74 (0.17), residues: 892 sheet: -1.85 (0.57), residues: 76 loop : -0.93 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1271 TYR 0.009 0.001 TYR A 217 PHE 0.028 0.001 PHE A1037 TRP 0.009 0.001 TRP A 309 HIS 0.003 0.001 HIS A1371 Details of bonding type rmsd covalent geometry : bond 0.00402 (11503) covalent geometry : angle 0.60336 (15604) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.13774 ( 2) hydrogen bonds : bond 0.04649 ( 623) hydrogen bonds : angle 5.22968 ( 1839) *********************** 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 211 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.594 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 75 LEU cc_start: 0.9733 (mp) cc_final: 0.9510 (mm) REVERT: A 172 TYR cc_start: 0.9564 (t80) cc_final: 0.9356 (t80) REVERT: A 243 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 246 MET cc_start: 0.9252 (tmm) cc_final: 0.8938 (tmm) REVERT: A 249 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9028 (mm-30) REVERT: A 419 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 496 ASP cc_start: 0.9042 (m-30) cc_final: 0.8704 (m-30) REVERT: A 611 GLU cc_start: 0.9445 (tm-30) cc_final: 0.8973 (tm-30) REVERT: A 616 TYR cc_start: 0.9741 (t80) cc_final: 0.9510 (t80) REVERT: A 687 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8744 (mp0) REVERT: A 757 LYS cc_start: 0.9753 (mtpp) cc_final: 0.9549 (mtmm) REVERT: A 822 MET cc_start: 0.9036 (mmp) cc_final: 0.8769 (mtp) REVERT: A 1069 MET cc_start: 0.9036 (mmm) cc_final: 0.8275 (tpp) REVERT: A 1097 GLN cc_start: 0.9492 (tm-30) cc_final: 0.9287 (tm-30) REVERT: A 1103 ILE cc_start: 0.9569 (mt) cc_final: 0.9300 (tp) REVERT: A 1118 MET cc_start: 0.9136 (mmm) cc_final: 0.8896 (mmm) REVERT: A 1202 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9148 (p) REVERT: A 1226 MET cc_start: 0.9537 (tpp) cc_final: 0.9221 (mmp) REVERT: A 1392 ARG cc_start: 0.9645 (OUTLIER) cc_final: 0.8823 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9793 (tt) cc_final: 0.9324 (mt) outliers start: 29 outliers final: 24 residues processed: 201 average time/residue: 0.2153 time to fit residues: 66.1383 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 : 0.623 ------------------------------------------------------------------------------- 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 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU 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 617 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU 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 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 29 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 129 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 117 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.053481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042677 restraints weight = 182758.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044595 restraints weight = 77655.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.045948 restraints weight = 44533.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.046911 restraints weight = 30080.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047606 restraints weight = 22363.432| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11504 Z= 0.130 Angle : 0.598 7.625 15606 Z= 0.306 Chirality : 0.038 0.142 1824 Planarity : 0.003 0.057 1924 Dihedral : 6.193 89.988 1552 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.08 % Allowed : 24.10 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1404 helix: 1.05 (0.17), residues: 892 sheet: -1.80 (0.57), residues: 76 loop : -0.85 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1271 TYR 0.008 0.001 TYR A 217 PHE 0.039 0.001 PHE A1037 TRP 0.007 0.001 TRP A 309 HIS 0.002 0.000 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00271 (11503) covalent geometry : angle 0.59847 (15604) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.18647 ( 2) hydrogen bonds : bond 0.04531 ( 623) hydrogen bonds : angle 4.90111 ( 1839) *********************** 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 204 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.679 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 75 LEU cc_start: 0.9725 (mp) cc_final: 0.9514 (mm) REVERT: A 172 TYR cc_start: 0.9536 (t80) cc_final: 0.9335 (t80) REVERT: A 243 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8589 (tm-30) REVERT: A 246 MET cc_start: 0.9218 (tmm) cc_final: 0.8853 (tmm) REVERT: A 249 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9001 (mm-30) REVERT: A 419 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 496 ASP cc_start: 0.9030 (m-30) cc_final: 0.8682 (m-30) REVERT: A 611 GLU cc_start: 0.9420 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 616 TYR cc_start: 0.9720 (t80) cc_final: 0.9470 (t80) REVERT: A 617 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9338 (mm) REVERT: A 687 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8733 (mp0) REVERT: A 756 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: A 757 LYS cc_start: 0.9737 (mtpp) cc_final: 0.9504 (mtmm) REVERT: A 822 MET cc_start: 0.9028 (mmp) cc_final: 0.8746 (mtp) REVERT: A 1069 MET cc_start: 0.8992 (mmm) cc_final: 0.8223 (tpp) REVERT: A 1097 GLN cc_start: 0.9476 (tm-30) cc_final: 0.9273 (tm-30) REVERT: A 1103 ILE cc_start: 0.9556 (mt) cc_final: 0.9280 (tp) REVERT: A 1118 MET cc_start: 0.9148 (mmm) cc_final: 0.8912 (mmm) REVERT: A 1226 MET cc_start: 0.9513 (tpp) cc_final: 0.9173 (mmp) REVERT: A 1392 ARG cc_start: 0.9644 (OUTLIER) cc_final: 0.8814 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9776 (tt) cc_final: 0.9310 (mt) outliers start: 26 outliers final: 22 residues processed: 195 average time/residue: 0.2108 time to fit residues: 63.2526 Evaluate side-chains 196 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU 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 617 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1107 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.053140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042441 restraints weight = 185002.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044342 restraints weight = 79312.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.045706 restraints weight = 45543.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046690 restraints weight = 30522.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.047356 restraints weight = 22486.256| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11504 Z= 0.165 Angle : 0.598 7.682 15606 Z= 0.311 Chirality : 0.038 0.142 1824 Planarity : 0.003 0.042 1924 Dihedral : 6.154 88.055 1552 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.32 % Allowed : 23.86 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.23), residues: 1404 helix: 1.12 (0.17), residues: 895 sheet: -1.75 (0.58), residues: 76 loop : -0.87 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1271 TYR 0.010 0.001 TYR A 217 PHE 0.022 0.001 PHE A1037 TRP 0.008 0.001 TRP A 309 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00328 (11503) covalent geometry : angle 0.59838 (15604) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.07434 ( 2) hydrogen bonds : bond 0.04376 ( 623) hydrogen bonds : angle 4.93979 ( 1839) *********************** 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 199 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.672 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: A 75 LEU cc_start: 0.9739 (mp) cc_final: 0.9524 (mm) REVERT: A 243 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 246 MET cc_start: 0.9226 (tmm) cc_final: 0.8769 (tmm) REVERT: A 419 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8714 (mt-10) REVERT: A 496 ASP cc_start: 0.9039 (m-30) cc_final: 0.8700 (m-30) REVERT: A 611 GLU cc_start: 0.9430 (tm-30) cc_final: 0.8929 (tm-30) REVERT: A 616 TYR cc_start: 0.9752 (t80) cc_final: 0.9535 (t80) REVERT: A 617 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9344 (mm) REVERT: A 687 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8758 (mp0) REVERT: A 756 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: A 757 LYS cc_start: 0.9738 (mtpp) cc_final: 0.9531 (mtmm) REVERT: A 822 MET cc_start: 0.8967 (mmp) cc_final: 0.8726 (mtp) REVERT: A 1069 MET cc_start: 0.8992 (mmm) cc_final: 0.8243 (tpp) REVERT: A 1097 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9273 (tm-30) REVERT: A 1103 ILE cc_start: 0.9566 (mt) cc_final: 0.9296 (tp) REVERT: A 1118 MET cc_start: 0.9157 (mmm) cc_final: 0.8919 (mmm) REVERT: A 1226 MET cc_start: 0.9511 (tpp) cc_final: 0.9170 (mmp) REVERT: A 1261 GLU cc_start: 0.9446 (tp30) cc_final: 0.9141 (tm-30) REVERT: A 1392 ARG cc_start: 0.9647 (OUTLIER) cc_final: 0.8807 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9772 (tt) cc_final: 0.9308 (mt) outliers start: 29 outliers final: 24 residues processed: 189 average time/residue: 0.2112 time to fit residues: 61.9583 Evaluate side-chains 193 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 222 THR 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 358 TRP Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 455 LEU 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 617 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1000 LEU 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 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 124 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.053236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042464 restraints weight = 180700.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044399 restraints weight = 76493.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045835 restraints weight = 43861.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.046775 restraints weight = 29166.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047472 restraints weight = 21730.879| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11504 Z= 0.116 Angle : 0.608 8.100 15606 Z= 0.305 Chirality : 0.039 0.143 1824 Planarity : 0.003 0.045 1924 Dihedral : 6.145 88.682 1552 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.08 % Allowed : 23.86 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.23), residues: 1404 helix: 1.36 (0.17), residues: 892 sheet: -1.69 (0.58), residues: 76 loop : -0.77 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.008 0.001 TYR A 217 PHE 0.029 0.001 PHE A1037 TRP 0.007 0.001 TRP A 517 HIS 0.002 0.000 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00251 (11503) covalent geometry : angle 0.60761 (15604) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.25151 ( 2) hydrogen bonds : bond 0.04379 ( 623) hydrogen bonds : angle 4.67898 ( 1839) ********************** 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 211 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.708 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: A 222 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9103 (p) REVERT: A 246 MET cc_start: 0.9197 (tmm) cc_final: 0.8991 (tmm) REVERT: A 492 MET cc_start: 0.9617 (mmp) cc_final: 0.9375 (mmp) REVERT: A 496 ASP cc_start: 0.8942 (m-30) cc_final: 0.8641 (m-30) REVERT: A 611 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8903 (tm-30) REVERT: A 616 TYR cc_start: 0.9707 (t80) cc_final: 0.9487 (t80) REVERT: A 756 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: A 757 LYS cc_start: 0.9727 (mtpp) cc_final: 0.9516 (mtmm) REVERT: A 822 MET cc_start: 0.8934 (mmp) cc_final: 0.8729 (mtp) REVERT: A 969 GLU cc_start: 0.9519 (tm-30) cc_final: 0.9289 (tm-30) REVERT: A 1097 GLN cc_start: 0.9462 (tm-30) cc_final: 0.9261 (tm-30) REVERT: A 1103 ILE cc_start: 0.9550 (mt) cc_final: 0.9274 (tp) REVERT: A 1116 ILE cc_start: 0.9498 (mt) cc_final: 0.9266 (tp) REVERT: A 1118 MET cc_start: 0.9184 (mmm) cc_final: 0.8946 (mmm) REVERT: A 1226 MET cc_start: 0.9468 (tpp) cc_final: 0.9124 (mmp) REVERT: A 1317 LEU cc_start: 0.9757 (tp) cc_final: 0.9496 (tt) REVERT: A 1392 ARG cc_start: 0.9640 (OUTLIER) cc_final: 0.8794 (tpt-90) REVERT: A 1458 LEU cc_start: 0.9768 (tt) cc_final: 0.9315 (mt) REVERT: A 1489 ILE cc_start: 0.9803 (mp) cc_final: 0.9515 (tp) outliers start: 26 outliers final: 22 residues processed: 201 average time/residue: 0.2244 time to fit residues: 69.1688 Evaluate side-chains 200 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 222 THR 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 358 TRP Chi-restraints excluded: chain A residue 385 CYS 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 756 GLU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1194 GLN 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 8 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.053070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.042420 restraints weight = 182541.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044316 restraints weight = 78256.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045688 restraints weight = 45194.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046654 restraints weight = 30375.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047360 restraints weight = 22539.692| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11504 Z= 0.138 Angle : 0.613 9.335 15606 Z= 0.313 Chirality : 0.038 0.146 1824 Planarity : 0.003 0.045 1924 Dihedral : 6.117 88.979 1552 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.08 % Allowed : 24.26 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.23), residues: 1404 helix: 1.40 (0.17), residues: 895 sheet: -1.73 (0.58), residues: 76 loop : -0.78 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1271 TYR 0.011 0.001 TYR A 217 PHE 0.055 0.001 PHE A1037 TRP 0.006 0.001 TRP A 709 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00286 (11503) covalent geometry : angle 0.61345 (15604) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.11121 ( 2) hydrogen bonds : bond 0.04273 ( 623) hydrogen bonds : angle 4.74174 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.22 seconds wall clock time: 62 minutes 46.74 seconds (3766.74 seconds total)