Starting phenix.real_space_refine on Sun Sep 13 08:15:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4a_65623/09_2026/9w4a_65623.map" } resolution = 4.25 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= -0.088 sd= 0.643 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13432 2.51 5 N 3676 2.21 5 O 4002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10599 Classifications: {'peptide': 1361} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1304} Chain breaks: 1 Chain: "B" Number of atoms: 10599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10599 Classifications: {'peptide': 1361} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1304} Chain breaks: 1 Time building chain proxies: 5.10, per 1000 atoms: 0.24 Number of scatterers: 21198 At special positions: 0 Unit cell: (121.83, 186.93, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4002 8.00 N 3676 7.00 C 13432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5096 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 20 sheets defined 55.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 18 through 31 removed outlier: 4.233A pdb=" N GLU A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 64 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 73 through 79 removed outlier: 4.318A pdb=" N THR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 136 through 153 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.702A pdb=" N LYS A 183 " --> pdb=" O HIS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.593A pdb=" N ILE A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 305 through 320 removed outlier: 3.813A pdb=" N GLU A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.590A pdb=" N LEU A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.708A pdb=" N SER A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.940A pdb=" N ALA A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 425 removed outlier: 3.582A pdb=" N LEU A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 465 removed outlier: 3.545A pdb=" N LEU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.977A pdb=" N ASN A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 3.988A pdb=" N GLU A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 521 " --> pdb=" O HIS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.965A pdb=" N ILE A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.584A pdb=" N TRP A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 649 through 674 Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 706 through 717 Processing helix chain 'A' and resid 749 through 753 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 786 through 794 removed outlier: 7.736A pdb=" N ALA A 791 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 793 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 812 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.915A pdb=" N GLN A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.571A pdb=" N HIS A 834 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 905 through 916 Processing helix chain 'A' and resid 932 through 937 removed outlier: 4.206A pdb=" N LEU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 962 Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.707A pdb=" N MET A 975 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 996 through 1000 Processing helix chain 'A' and resid 1003 through 1014 Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.773A pdb=" N ASN A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1081 through 1093 Processing helix chain 'A' and resid 1114 through 1134 removed outlier: 3.708A pdb=" N ILE A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY A1120 " --> pdb=" O GLU A1116 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1207 Processing helix chain 'A' and resid 1238 through 1247 removed outlier: 4.337A pdb=" N THR A1242 " --> pdb=" O ALA A1238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A1247 " --> pdb=" O GLU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 Processing helix chain 'A' and resid 1341 through 1356 Processing helix chain 'A' and resid 1364 through 1372 removed outlier: 3.810A pdb=" N LEU A1370 " --> pdb=" O PRO A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1380 Processing helix chain 'A' and resid 1385 through 1392 removed outlier: 3.997A pdb=" N ARG A1389 " --> pdb=" O ASN A1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.581A pdb=" N GLU B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 136 through 153 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 205 through 213 Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.899A pdb=" N LYS B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.735A pdb=" N CYS B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 248 " --> pdb=" O TRP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 277 through 304 removed outlier: 3.541A pdb=" N ASN B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.654A pdb=" N PHE B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.531A pdb=" N LEU B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.659A pdb=" N SER B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 401 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.518A pdb=" N TYR B 408 " --> pdb=" O LYS B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 425 removed outlier: 3.744A pdb=" N ASP B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 465 Processing helix chain 'B' and resid 467 through 481 Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.739A pdb=" N THR B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.550A pdb=" N VAL B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.572A pdb=" N ILE B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 587 through 600 removed outlier: 3.995A pdb=" N TRP B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 620 through 628 Processing helix chain 'B' and resid 631 through 635 removed outlier: 3.676A pdb=" N TYR B 635 " --> pdb=" O HIS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 644 removed outlier: 4.273A pdb=" N ARG B 643 " --> pdb=" O ASN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 674 Processing helix chain 'B' and resid 677 through 685 removed outlier: 3.843A pdb=" N PHE B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 717 removed outlier: 3.901A pdb=" N SER B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 Processing helix chain 'B' and resid 755 through 773 Processing helix chain 'B' and resid 786 through 794 removed outlier: 3.708A pdb=" N GLU B 789 " --> pdb=" O GLN B 786 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA B 791 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 792 " --> pdb=" O GLU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 812 Processing helix chain 'B' and resid 860 through 864 Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 886 through 896 removed outlier: 4.265A pdb=" N ASN B 890 " --> pdb=" O GLU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 917 removed outlier: 3.545A pdb=" N THR B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 removed outlier: 3.681A pdb=" N LYS B 935 " --> pdb=" O ASP B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.666A pdb=" N THR B 976 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.604A pdb=" N LEU B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1000 Processing helix chain 'B' and resid 1003 through 1014 removed outlier: 3.653A pdb=" N VAL B1007 " --> pdb=" O ASN B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1039 removed outlier: 3.536A pdb=" N ALA B1033 " --> pdb=" O SER B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1056 Processing helix chain 'B' and resid 1056 through 1067 Processing helix chain 'B' and resid 1081 through 1093 Processing helix chain 'B' and resid 1114 through 1133 removed outlier: 4.677A pdb=" N ILE B1119 " --> pdb=" O PRO B1115 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1208 removed outlier: 3.511A pdb=" N ALA B1198 " --> pdb=" O LYS B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1247 removed outlier: 3.774A pdb=" N THR B1245 " --> pdb=" O VAL B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1258 Processing helix chain 'B' and resid 1341 through 1356 Processing helix chain 'B' and resid 1364 through 1374 Processing helix chain 'B' and resid 1374 through 1380 Processing helix chain 'B' and resid 1385 through 1393 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 102 removed outlier: 6.893A pdb=" N GLU A 109 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 99 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER A 107 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS A 101 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL A 158 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 122 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 160 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 124 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 162 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLN A 126 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR A 163 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA A 202 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A 224 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLY A 201 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASN A 226 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY A 203 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 6.893A pdb=" N GLU A 109 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 99 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER A 107 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS A 101 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL A 158 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 122 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 160 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 124 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 162 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLN A 126 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR A 163 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA A 202 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR A 195 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 218 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY A 197 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU A 220 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 199 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE A 268 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER A 219 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA4, first strand: chain 'A' and resid 687 through 691 removed outlier: 5.290A pdb=" N HIS A 688 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 730 " --> pdb=" O HIS A 688 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 736 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 781 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 776 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N PHE A 818 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS A 778 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE A 820 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 780 " --> pdb=" O PHE A 820 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP A 822 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY A 821 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 839 " --> pdb=" O GLY A 878 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 880 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR A 841 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 988 through 991 removed outlier: 4.215A pdb=" N VAL A 969 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS A 942 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A1020 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 944 " --> pdb=" O HIS A1020 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1110 through 1112 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1232 removed outlier: 5.889A pdb=" N VAL A1226 " --> pdb=" O ASN A1220 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A1220 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE A1228 " --> pdb=" O ILE A1218 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE A1218 " --> pdb=" O PHE A1228 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A1230 " --> pdb=" O GLU A1216 " (cutoff:3.500A) removed outlier: 12.969A pdb=" N LEU A1147 " --> pdb=" O VAL A1172 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A1172 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1149 " --> pdb=" O CYS A1170 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY A1166 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A1155 " --> pdb=" O VAL A1164 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A1164 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS A1170 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU A1181 " --> pdb=" O CYS A1170 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A1172 " --> pdb=" O VAL A1179 " (cutoff:3.500A) removed outlier: 14.057A pdb=" N GLN A1177 " --> pdb=" O THR A1280 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A1280 " --> pdb=" O GLN A1177 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A1179 " --> pdb=" O ARG A1278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1282 through 1286 Processing sheet with id=AA9, first strand: chain 'A' and resid 1299 through 1300 Processing sheet with id=AB1, first strand: chain 'A' and resid 1304 through 1305 Processing sheet with id=AB2, first strand: chain 'B' and resid 95 through 102 removed outlier: 7.054A pdb=" N GLU B 109 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU B 99 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER B 107 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS B 101 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL B 158 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY B 122 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU B 160 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 124 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 195 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 218 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY B 197 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 220 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 199 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 217 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE B 268 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 219 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.020A pdb=" N GLY B 203 " --> pdb=" O ASN B 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 366 through 367 Processing sheet with id=AB5, first strand: chain 'B' and resid 686 through 691 removed outlier: 4.315A pdb=" N PHE B 689 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 728 " --> pdb=" O PHE B 689 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU B 691 " --> pdb=" O THR B 726 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 726 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL B 777 " --> pdb=" O ARG B 739 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 741 " --> pdb=" O VAL B 777 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE B 779 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 743 " --> pdb=" O PHE B 779 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 815 " --> pdb=" O GLN B 838 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR B 840 " --> pdb=" O VAL B 815 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET B 817 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 842 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B 819 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL B 880 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR B 841 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 988 through 991 removed outlier: 6.753A pdb=" N VAL B 966 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL B 990 " --> pdb=" O VAL B 966 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 968 " --> pdb=" O VAL B 990 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 969 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 942 " --> pdb=" O ALA B1018 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS B1020 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 944 " --> pdb=" O HIS B1020 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1110 through 1112 Processing sheet with id=AB8, first strand: chain 'B' and resid 1225 through 1232 removed outlier: 5.623A pdb=" N VAL B1226 " --> pdb=" O ASN B1220 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B1220 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE B1228 " --> pdb=" O ILE B1218 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE B1218 " --> pdb=" O PHE B1228 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU B1147 " --> pdb=" O SER B1171 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER B1171 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N HIS B1149 " --> pdb=" O ASP B1169 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP B1169 " --> pdb=" O HIS B1149 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B1151 " --> pdb=" O LEU B1167 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B1167 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B1153 " --> pdb=" O LEU B1165 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B1171 " --> pdb=" O VAL B1180 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B1180 " --> pdb=" O SER B1171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN B1173 " --> pdb=" O LYS B1178 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS B1178 " --> pdb=" O GLN B1173 " (cutoff:3.500A) removed outlier: 13.869A pdb=" N GLN B1177 " --> pdb=" O THR B1280 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N THR B1280 " --> pdb=" O GLN B1177 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1179 " --> pdb=" O ARG B1278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1282 through 1286 Processing sheet with id=AC1, first strand: chain 'B' and resid 1299 through 1300 Processing sheet with id=AC2, first strand: chain 'B' and resid 1304 through 1305 1134 hydrogen bonds defined for protein. 3246 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: 5.08 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4905 1.34 - 1.46: 5131 1.46 - 1.58: 11430 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 21616 Sorted by residual: bond pdb=" CA LYS B 938 " pdb=" C LYS B 938 " ideal model delta sigma weight residual 1.518 1.551 -0.034 9.60e-03 1.09e+04 1.22e+01 bond pdb=" CA VAL B 872 " pdb=" C VAL B 872 " ideal model delta sigma weight residual 1.526 1.554 -0.027 7.90e-03 1.60e+04 1.19e+01 bond pdb=" CA ASP B 972 " pdb=" C ASP B 972 " ideal model delta sigma weight residual 1.520 1.559 -0.038 1.23e-02 6.61e+03 9.66e+00 bond pdb=" CA ILE B 209 " pdb=" C ILE B 209 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.05e-02 9.07e+03 9.22e+00 bond pdb=" CA MET A 847 " pdb=" C MET A 847 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.26e-02 6.30e+03 8.47e+00 ... (remaining 21611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21576 2.07 - 4.14: 6132 4.14 - 6.20: 1465 6.20 - 8.27: 101 8.27 - 10.34: 10 Bond angle restraints: 29284 Sorted by residual: angle pdb=" CA ASP B 972 " pdb=" CB ASP B 972 " pdb=" CG ASP B 972 " ideal model delta sigma weight residual 112.60 121.74 -9.14 1.00e+00 1.00e+00 8.36e+01 angle pdb=" CA ASP A1287 " pdb=" CB ASP A1287 " pdb=" CG ASP A1287 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.00e+00 1.00e+00 6.12e+01 angle pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " pdb=" CG ASN A 607 " ideal model delta sigma weight residual 112.60 120.37 -7.77 1.00e+00 1.00e+00 6.04e+01 angle pdb=" CA ASP B 730 " pdb=" CB ASP B 730 " pdb=" CG ASP B 730 " ideal model delta sigma weight residual 112.60 120.26 -7.66 1.00e+00 1.00e+00 5.86e+01 angle pdb=" CA ASN B 607 " pdb=" CB ASN B 607 " pdb=" CG ASN B 607 " ideal model delta sigma weight residual 112.60 120.25 -7.65 1.00e+00 1.00e+00 5.85e+01 ... (remaining 29279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12235 17.99 - 35.97: 606 35.97 - 53.96: 117 53.96 - 71.94: 73 71.94 - 89.93: 61 Dihedral angle restraints: 13092 sinusoidal: 5194 harmonic: 7898 Sorted by residual: dihedral pdb=" C ASN A 241 " pdb=" N ASN A 241 " pdb=" CA ASN A 241 " pdb=" CB ASN A 241 " ideal model delta harmonic sigma weight residual -122.60 -151.35 28.75 0 2.50e+00 1.60e-01 1.32e+02 dihedral pdb=" N ASN A 241 " pdb=" C ASN A 241 " pdb=" CA ASN A 241 " pdb=" CB ASN A 241 " ideal model delta harmonic sigma weight residual 122.80 150.88 -28.08 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" CA ASP A 91 " pdb=" C ASP A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 3154 0.231 - 0.462: 146 0.462 - 0.694: 1 0.694 - 0.925: 0 0.925 - 1.156: 1 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA ASN A 241 " pdb=" N ASN A 241 " pdb=" C ASN A 241 " pdb=" CB ASN A 241 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CA HIS A1239 " pdb=" N HIS A1239 " pdb=" C HIS A1239 " pdb=" CB HIS A1239 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ILE A 725 " pdb=" N ILE A 725 " pdb=" C ILE A 725 " pdb=" CB ILE A 725 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 3299 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.108 2.00e-02 2.50e+03 6.25e-02 7.81e+01 pdb=" CG TYR A 351 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 522 " 0.107 2.00e-02 2.50e+03 6.56e-02 7.53e+01 pdb=" CG PHE B 522 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 PHE B 522 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE B 522 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 PHE B 522 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 522 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE B 522 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 522 " 0.106 2.00e-02 2.50e+03 6.49e-02 7.37e+01 pdb=" CG PHE A 522 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE A 522 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 522 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE A 522 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 522 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 522 " 0.053 2.00e-02 2.50e+03 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2181 2.83 - 3.35: 21716 3.35 - 3.87: 34917 3.87 - 4.38: 44349 4.38 - 4.90: 71560 Nonbonded interactions: 174723 Sorted by model distance: nonbonded pdb=" CE1 PHE A 762 " pdb=" CD1 LEU A 766 " model vdw 2.313 3.760 nonbonded pdb=" CZ PHE A 762 " pdb=" CD1 ILE A 804 " model vdw 2.320 3.760 nonbonded pdb=" O VAL A 593 " pdb=" OE2 GLU A 596 " model vdw 2.323 3.040 nonbonded pdb=" O TYR A 240 " pdb=" OD1 ASN A 241 " model vdw 2.329 3.040 nonbonded pdb=" O MET A1187 " pdb=" OH TYR A1219 " model vdw 2.378 3.040 ... (remaining 174718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.240 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.015 0.043 21616 Z= 0.893 Angle : 1.992 10.339 29284 Z= 1.417 Chirality : 0.110 1.156 3302 Planarity : 0.012 0.099 3816 Dihedral : 14.536 89.926 7996 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.70 % Allowed : 2.79 % Favored : 96.51 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 2714 helix: -1.43 (0.11), residues: 1324 sheet: -1.35 (0.30), residues: 262 loop : -0.99 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG A1174 TYR 0.108 0.017 TYR A 351 PHE 0.107 0.019 PHE B 522 TRP 0.108 0.020 TRP B 399 HIS 0.018 0.004 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.01486 / 0.89 (21616) covalent geometry : angle 1.99195 / 1.42 (29284) hydrogen bonds : bond 0.21917 / 14.58 ( 1118) hydrogen bonds : angle 8.29810 / 5.92 ( 3246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 703 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9469 (mt) cc_final: 0.9181 (pp) REVERT: A 91 ASP cc_start: 0.9422 (m-30) cc_final: 0.9028 (p0) REVERT: A 145 LYS cc_start: 0.9569 (tttp) cc_final: 0.9339 (mmtt) REVERT: A 150 PHE cc_start: 0.8987 (m-80) cc_final: 0.8771 (m-80) REVERT: A 170 GLU cc_start: 0.9193 (pt0) cc_final: 0.8784 (tm-30) REVERT: A 256 GLU cc_start: 0.9384 (mp0) cc_final: 0.9123 (pm20) REVERT: A 257 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9097 (mt-10) REVERT: A 284 ARG cc_start: 0.9501 (mtt180) cc_final: 0.9105 (ptp-170) REVERT: A 287 ILE cc_start: 0.9499 (mt) cc_final: 0.9019 (pt) REVERT: A 303 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9133 (mp0) REVERT: A 324 ASN cc_start: 0.9527 (m-40) cc_final: 0.9285 (p0) REVERT: A 354 LEU cc_start: 0.9262 (mt) cc_final: 0.9061 (mt) REVERT: A 465 LYS cc_start: 0.9431 (mtmm) cc_final: 0.9092 (mtpt) REVERT: A 656 MET cc_start: 0.9452 (mtp) cc_final: 0.9243 (tpt) REVERT: A 667 LEU cc_start: 0.9652 (mt) cc_final: 0.9275 (pp) REVERT: A 671 LYS cc_start: 0.9720 (mttt) cc_final: 0.9501 (mttt) REVERT: A 697 MET cc_start: 0.9303 (ptm) cc_final: 0.8660 (ppp) REVERT: A 785 MET cc_start: 0.8212 (mmm) cc_final: 0.7488 (tpt) REVERT: A 818 PHE cc_start: 0.8806 (m-80) cc_final: 0.8105 (m-10) REVERT: A 820 PHE cc_start: 0.8567 (p90) cc_final: 0.7999 (p90) REVERT: A 854 VAL cc_start: 0.9211 (t) cc_final: 0.8816 (t) REVERT: A 899 MET cc_start: 0.7970 (ttm) cc_final: 0.7707 (mtp) REVERT: A 935 LYS cc_start: 0.8959 (mttt) cc_final: 0.8574 (pttt) REVERT: A 951 THR cc_start: 0.9316 (m) cc_final: 0.9075 (p) REVERT: A 960 HIS cc_start: 0.8291 (m90) cc_final: 0.7359 (m-70) REVERT: A 1020 HIS cc_start: 0.8439 (t-90) cc_final: 0.8217 (t-90) REVERT: A 1061 ILE cc_start: 0.9522 (mt) cc_final: 0.9215 (tt) REVERT: A 1107 LYS cc_start: 0.9557 (mmtp) cc_final: 0.9199 (tptp) REVERT: A 1180 VAL cc_start: 0.9188 (t) cc_final: 0.8961 (p) REVERT: A 1218 ILE cc_start: 0.8910 (mt) cc_final: 0.8655 (mm) REVERT: A 1225 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9263 (mp0) REVERT: A 1229 MET cc_start: 0.9630 (ttp) cc_final: 0.9416 (ptt) REVERT: A 1235 LEU cc_start: 0.8669 (tp) cc_final: 0.8367 (tp) REVERT: A 1309 HIS cc_start: 0.7358 (t-90) cc_final: 0.6919 (t70) REVERT: A 1324 VAL cc_start: 0.8253 (t) cc_final: 0.7932 (p) REVERT: A 1329 ASP cc_start: 0.9606 (p0) cc_final: 0.9325 (p0) REVERT: A 1343 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8944 (mm-30) REVERT: A 1382 TYR cc_start: 0.8444 (p90) cc_final: 0.8228 (p90) REVERT: B 49 LEU cc_start: 0.8733 (mt) cc_final: 0.8484 (mt) REVERT: B 72 LYS cc_start: 0.9343 (tttp) cc_final: 0.9074 (tttp) REVERT: B 95 ARG cc_start: 0.9505 (ttt180) cc_final: 0.9303 (ttt180) REVERT: B 112 LEU cc_start: 0.9258 (tp) cc_final: 0.8918 (tt) REVERT: B 132 ASN cc_start: 0.9290 (m-40) cc_final: 0.8831 (t0) REVERT: B 155 MET cc_start: 0.6130 (mtt) cc_final: 0.5911 (ttp) REVERT: B 158 VAL cc_start: 0.9240 (t) cc_final: 0.8984 (t) REVERT: B 161 ILE cc_start: 0.7758 (mp) cc_final: 0.7262 (tp) REVERT: B 251 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7069 (p) REVERT: B 259 TYR cc_start: 0.9090 (t80) cc_final: 0.8572 (t80) REVERT: B 291 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9140 (pt0) REVERT: B 299 ASN cc_start: 0.9456 (m-40) cc_final: 0.9237 (m110) REVERT: B 363 ILE cc_start: 0.9182 (pt) cc_final: 0.8544 (mm) REVERT: B 409 ASP cc_start: 0.9057 (m-30) cc_final: 0.8807 (p0) REVERT: B 461 TYR cc_start: 0.7881 (t80) cc_final: 0.7483 (t80) REVERT: B 532 SER cc_start: 0.9410 (m) cc_final: 0.9160 (p) REVERT: B 599 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9038 (mmtp) REVERT: B 603 PHE cc_start: 0.9367 (m-80) cc_final: 0.9122 (m-80) REVERT: B 693 ASN cc_start: 0.9189 (m110) cc_final: 0.8810 (m-40) REVERT: B 697 MET cc_start: 0.8608 (ptm) cc_final: 0.8390 (ptm) REVERT: B 739 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8700 (mmt180) REVERT: B 754 PHE cc_start: 0.8399 (t80) cc_final: 0.7758 (t80) REVERT: B 756 MET cc_start: 0.8423 (mtm) cc_final: 0.6870 (mtm) REVERT: B 765 LEU cc_start: 0.9440 (tp) cc_final: 0.8888 (mm) REVERT: B 777 VAL cc_start: 0.9362 (t) cc_final: 0.8736 (p) REVERT: B 822 ASP cc_start: 0.9206 (m-30) cc_final: 0.8670 (t70) REVERT: B 836 LEU cc_start: 0.9230 (mt) cc_final: 0.9001 (mp) REVERT: B 892 LEU cc_start: 0.9872 (mt) cc_final: 0.9635 (mt) REVERT: B 905 LYS cc_start: 0.9349 (mttt) cc_final: 0.8891 (mmtm) REVERT: B 917 LEU cc_start: 0.8897 (pp) cc_final: 0.8668 (pp) REVERT: B 931 ASN cc_start: 0.9094 (m-40) cc_final: 0.8250 (t0) REVERT: B 999 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9120 (mt-10) REVERT: B 1107 LYS cc_start: 0.9474 (mttt) cc_final: 0.9068 (tptp) REVERT: B 1113 LYS cc_start: 0.9356 (mttt) cc_final: 0.9124 (mmmt) REVERT: B 1118 MET cc_start: 0.8358 (tpp) cc_final: 0.7485 (ttm) REVERT: B 1235 LEU cc_start: 0.8248 (tp) cc_final: 0.8027 (mt) REVERT: B 1255 PHE cc_start: 0.8473 (m-80) cc_final: 0.8056 (m-10) REVERT: B 1275 MET cc_start: 0.8856 (ttm) cc_final: 0.8233 (tpp) outliers start: 16 outliers final: 4 residues processed: 719 average time/residue: 0.1849 time to fit residues: 192.9623 Evaluate side-chains 434 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 429 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS A 389 GLN A 470 ASN A 471 ASN A 477 GLN A 495 ASN A 496 GLN A 528 ASN A 585 GLN A 597 GLN A 659 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN A 946 HIS A1149 HIS A1153 GLN A1254 GLN B 280 HIS B 368 GLN B 389 GLN B 390 GLN B 392 GLN B 470 ASN B 528 ASN B 552 ASN B 553 ASN ** B 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN B1049 HIS B1059 ASN B1254 GLN B1293 GLN B1350 HIS B1385 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.044192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032736 restraints weight = 158442.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.034247 restraints weight = 108089.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.035436 restraints weight = 79409.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036379 restraints weight = 61280.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.037137 restraints weight = 49070.973| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21616 Z= 0.209 Angle : 0.713 9.498 29284 Z= 0.381 Chirality : 0.045 0.230 3302 Planarity : 0.005 0.057 3816 Dihedral : 4.997 25.982 2928 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2714 helix: 0.68 (0.13), residues: 1386 sheet: -0.49 (0.28), residues: 334 loop : -0.06 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 668 TYR 0.028 0.002 TYR A 353 PHE 0.029 0.003 PHE B 686 TRP 0.016 0.002 TRP B 399 HIS 0.008 0.002 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (21616) covalent geometry : angle 0.71338 / 0.38 (29284) hydrogen bonds : bond 0.04552 / 3.06 ( 1118) hydrogen bonds : angle 5.31188 / 3.74 ( 3246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 453 time to evaluate : 0.816 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 112 LEU cc_start: 0.8461 (tp) cc_final: 0.8147 (tt) REVERT: A 170 GLU cc_start: 0.9318 (pt0) cc_final: 0.8987 (tm-30) REVERT: A 256 GLU cc_start: 0.9400 (mp0) cc_final: 0.9186 (mp0) REVERT: A 317 ARG cc_start: 0.9279 (ttp-170) cc_final: 0.8133 (tpt170) REVERT: A 324 ASN cc_start: 0.9523 (m-40) cc_final: 0.9159 (p0) REVERT: A 326 MET cc_start: 0.9505 (ptm) cc_final: 0.9117 (ptm) REVERT: A 404 ASP cc_start: 0.8546 (t0) cc_final: 0.8139 (t0) REVERT: A 533 LEU cc_start: 0.9359 (tp) cc_final: 0.8898 (mt) REVERT: A 539 GLU cc_start: 0.9370 (pt0) cc_final: 0.8935 (tm-30) REVERT: A 572 LYS cc_start: 0.9379 (ttpt) cc_final: 0.9096 (tttt) REVERT: A 625 TYR cc_start: 0.8966 (t80) cc_final: 0.8747 (t80) REVERT: A 667 LEU cc_start: 0.9624 (mt) cc_final: 0.9414 (pp) REVERT: A 697 MET cc_start: 0.8769 (ptm) cc_final: 0.8353 (ptm) REVERT: A 756 MET cc_start: 0.7613 (mtm) cc_final: 0.7243 (mtt) REVERT: A 785 MET cc_start: 0.8531 (mmm) cc_final: 0.8250 (mmm) REVERT: A 804 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 846 ASN cc_start: 0.9209 (t0) cc_final: 0.8975 (t0) REVERT: A 854 VAL cc_start: 0.9245 (t) cc_final: 0.8995 (t) REVERT: A 889 ASP cc_start: 0.9277 (m-30) cc_final: 0.9054 (m-30) REVERT: A 1028 GLU cc_start: 0.8774 (tt0) cc_final: 0.8520 (tp30) REVERT: A 1107 LYS cc_start: 0.9585 (mmtp) cc_final: 0.9075 (tptp) REVERT: A 1118 MET cc_start: 0.7469 (ttt) cc_final: 0.6636 (ttt) REVERT: A 1180 VAL cc_start: 0.9482 (t) cc_final: 0.9267 (p) REVERT: A 1187 MET cc_start: 0.9095 (mtt) cc_final: 0.8886 (mtt) REVERT: A 1229 MET cc_start: 0.9586 (ttp) cc_final: 0.9278 (tmm) REVERT: A 1251 VAL cc_start: 0.9532 (t) cc_final: 0.9319 (t) REVERT: A 1255 PHE cc_start: 0.7891 (m-10) cc_final: 0.7407 (m-80) REVERT: A 1343 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9051 (mm-30) REVERT: B 49 LEU cc_start: 0.8872 (mt) cc_final: 0.8512 (mp) REVERT: B 95 ARG cc_start: 0.9440 (ttt180) cc_final: 0.9179 (ttt180) REVERT: B 114 PHE cc_start: 0.9008 (m-80) cc_final: 0.8726 (m-10) REVERT: B 132 ASN cc_start: 0.9129 (m-40) cc_final: 0.8767 (t0) REVERT: B 259 TYR cc_start: 0.9075 (t80) cc_final: 0.8685 (t80) REVERT: B 290 ILE cc_start: 0.9849 (mt) cc_final: 0.9460 (tp) REVERT: B 291 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9198 (mm-30) REVERT: B 467 ASN cc_start: 0.9391 (p0) cc_final: 0.9148 (p0) REVERT: B 561 HIS cc_start: 0.9405 (t-90) cc_final: 0.9177 (t-90) REVERT: B 603 PHE cc_start: 0.9328 (m-80) cc_final: 0.9064 (m-80) REVERT: B 656 MET cc_start: 0.9493 (mpp) cc_final: 0.9191 (ptp) REVERT: B 739 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8194 (mmm-85) REVERT: B 756 MET cc_start: 0.8632 (mtm) cc_final: 0.8220 (mtt) REVERT: B 818 PHE cc_start: 0.8046 (m-80) cc_final: 0.7755 (m-80) REVERT: B 831 PHE cc_start: 0.8893 (p90) cc_final: 0.8577 (p90) REVERT: B 931 ASN cc_start: 0.9389 (m-40) cc_final: 0.8493 (t0) REVERT: B 956 ILE cc_start: 0.9093 (pt) cc_final: 0.8710 (pt) REVERT: B 1118 MET cc_start: 0.8582 (tpp) cc_final: 0.7711 (ttm) REVERT: B 1187 MET cc_start: 0.8196 (mtt) cc_final: 0.7936 (mtt) REVERT: B 1205 ASP cc_start: 0.8957 (p0) cc_final: 0.8733 (p0) REVERT: B 1255 PHE cc_start: 0.8732 (m-80) cc_final: 0.8279 (m-10) REVERT: B 1275 MET cc_start: 0.8948 (ttm) cc_final: 0.8559 (tpp) outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.1750 time to fit residues: 118.0195 Evaluate side-chains 311 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 124 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 HIS A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 703 ASN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.042683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.031613 restraints weight = 164882.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.033095 restraints weight = 111401.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.034241 restraints weight = 81278.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.035147 restraints weight = 62575.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.035877 restraints weight = 50070.143| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21616 Z= 0.179 Angle : 0.649 7.858 29284 Z= 0.347 Chirality : 0.044 0.216 3302 Planarity : 0.005 0.047 3816 Dihedral : 4.815 24.410 2928 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.16), residues: 2714 helix: 1.27 (0.14), residues: 1342 sheet: -0.34 (0.29), residues: 324 loop : 0.01 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 720 TYR 0.028 0.002 TYR B1386 PHE 0.024 0.002 PHE A 30 TRP 0.019 0.002 TRP A 651 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (21616) covalent geometry : angle 0.64911 / 0.35 (29284) hydrogen bonds : bond 0.04059 / 2.71 ( 1118) hydrogen bonds : angle 5.11654 / 3.57 ( 3246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 0.749 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 61 LEU cc_start: 0.9562 (mt) cc_final: 0.9197 (mt) REVERT: A 95 ARG cc_start: 0.9456 (ptt90) cc_final: 0.9198 (ttp-110) REVERT: A 112 LEU cc_start: 0.8690 (tp) cc_final: 0.8420 (tt) REVERT: A 256 GLU cc_start: 0.9378 (mp0) cc_final: 0.8999 (pm20) REVERT: A 290 ILE cc_start: 0.9802 (OUTLIER) cc_final: 0.9563 (mm) REVERT: A 317 ARG cc_start: 0.9293 (ttp-170) cc_final: 0.8205 (tpt170) REVERT: A 324 ASN cc_start: 0.9518 (m-40) cc_final: 0.9172 (p0) REVERT: A 326 MET cc_start: 0.9515 (ptm) cc_final: 0.9288 (ptm) REVERT: A 510 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9295 (pm20) REVERT: A 533 LEU cc_start: 0.9368 (tp) cc_final: 0.8821 (mt) REVERT: A 572 LYS cc_start: 0.9405 (ttpt) cc_final: 0.9137 (tttt) REVERT: A 656 MET cc_start: 0.9419 (tpt) cc_final: 0.8978 (tpt) REVERT: A 697 MET cc_start: 0.8875 (ptm) cc_final: 0.8333 (ptm) REVERT: A 756 MET cc_start: 0.7545 (mtm) cc_final: 0.7126 (mtt) REVERT: A 804 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9048 (mp) REVERT: A 817 MET cc_start: 0.8573 (mmp) cc_final: 0.8368 (mmm) REVERT: A 818 PHE cc_start: 0.8534 (m-80) cc_final: 0.7940 (m-80) REVERT: A 846 ASN cc_start: 0.9218 (t0) cc_final: 0.9012 (t0) REVERT: A 901 MET cc_start: 0.8876 (mmp) cc_final: 0.8508 (mmp) REVERT: A 937 MET cc_start: 0.7998 (mtm) cc_final: 0.7796 (mtt) REVERT: A 1028 GLU cc_start: 0.8724 (tt0) cc_final: 0.8358 (tp30) REVERT: A 1118 MET cc_start: 0.7397 (ttt) cc_final: 0.6565 (ttt) REVERT: A 1151 GLU cc_start: 0.9317 (pt0) cc_final: 0.8736 (pm20) REVERT: A 1187 MET cc_start: 0.9122 (mtt) cc_final: 0.8854 (mtt) REVERT: A 1190 ASP cc_start: 0.9790 (m-30) cc_final: 0.9395 (p0) REVERT: A 1229 MET cc_start: 0.9638 (ttp) cc_final: 0.9408 (mtp) REVERT: A 1251 VAL cc_start: 0.9559 (t) cc_final: 0.9358 (t) REVERT: A 1255 PHE cc_start: 0.8047 (m-10) cc_final: 0.7553 (m-80) REVERT: A 1286 LEU cc_start: 0.9673 (mt) cc_final: 0.9459 (mt) REVERT: A 1343 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9087 (mm-30) REVERT: A 1382 TYR cc_start: 0.8428 (p90) cc_final: 0.7694 (p90) REVERT: B 49 LEU cc_start: 0.8891 (mt) cc_final: 0.8675 (mp) REVERT: B 95 ARG cc_start: 0.9408 (ttt180) cc_final: 0.9171 (ttt180) REVERT: B 109 GLU cc_start: 0.8678 (tt0) cc_final: 0.8347 (mp0) REVERT: B 132 ASN cc_start: 0.9164 (m-40) cc_final: 0.8800 (t0) REVERT: B 145 LYS cc_start: 0.9609 (pptt) cc_final: 0.9401 (pptt) REVERT: B 157 ILE cc_start: 0.9599 (mt) cc_final: 0.9307 (mm) REVERT: B 259 TYR cc_start: 0.9114 (t80) cc_final: 0.8856 (t80) REVERT: B 291 GLU cc_start: 0.9469 (mt-10) cc_final: 0.8885 (pt0) REVERT: B 295 ARG cc_start: 0.9567 (ptp-110) cc_final: 0.9137 (ptt-90) REVERT: B 299 ASN cc_start: 0.9527 (m110) cc_final: 0.9232 (m110) REVERT: B 467 ASN cc_start: 0.9441 (p0) cc_final: 0.9208 (p0) REVERT: B 561 HIS cc_start: 0.9405 (t-90) cc_final: 0.9181 (t-90) REVERT: B 603 PHE cc_start: 0.9285 (m-80) cc_final: 0.9003 (m-80) REVERT: B 769 CYS cc_start: 0.9495 (m) cc_final: 0.9258 (m) REVERT: B 899 MET cc_start: 0.8077 (mmp) cc_final: 0.7501 (mmm) REVERT: B 1051 MET cc_start: 0.9324 (ptt) cc_final: 0.8826 (ppp) REVERT: B 1054 MET cc_start: 0.8482 (mmp) cc_final: 0.8079 (mtm) REVERT: B 1059 ASN cc_start: 0.9653 (m110) cc_final: 0.9443 (m110) REVERT: B 1118 MET cc_start: 0.8455 (tpp) cc_final: 0.7554 (ttm) REVERT: B 1176 ASN cc_start: 0.9274 (m-40) cc_final: 0.8866 (t0) REVERT: B 1255 PHE cc_start: 0.8838 (m-80) cc_final: 0.8417 (m-10) outliers start: 3 outliers final: 0 residues processed: 388 average time/residue: 0.1675 time to fit residues: 97.1609 Evaluate side-chains 293 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 142 optimal weight: 0.0970 chunk 268 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 496 GLN A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 299 ASN B 418 ASN B 811 ASN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.041846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.030952 restraints weight = 165491.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.032413 restraints weight = 111858.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033550 restraints weight = 81682.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.034451 restraints weight = 62752.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.035113 restraints weight = 50161.553| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21616 Z= 0.170 Angle : 0.624 8.367 29284 Z= 0.331 Chirality : 0.044 0.214 3302 Planarity : 0.004 0.052 3816 Dihedral : 4.645 24.024 2928 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2714 helix: 1.34 (0.14), residues: 1360 sheet: -0.24 (0.28), residues: 334 loop : -0.01 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 394 TYR 0.028 0.002 TYR B1386 PHE 0.022 0.002 PHE A 762 TRP 0.018 0.002 TRP A 651 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (21616) covalent geometry : angle 0.62390 / 0.33 (29284) hydrogen bonds : bond 0.03743 / 2.53 ( 1118) hydrogen bonds : angle 5.07761 / 3.57 ( 3246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 0.847 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 183 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7641 (tttp) REVERT: A 238 ARG cc_start: 0.8802 (mmp80) cc_final: 0.8581 (mmp80) REVERT: A 256 GLU cc_start: 0.9348 (mp0) cc_final: 0.9121 (mp0) REVERT: A 257 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8757 (mt-10) REVERT: A 317 ARG cc_start: 0.9277 (ttp-170) cc_final: 0.8249 (tpt170) REVERT: A 324 ASN cc_start: 0.9516 (m-40) cc_final: 0.9189 (p0) REVERT: A 326 MET cc_start: 0.9511 (ptm) cc_final: 0.9155 (ptm) REVERT: A 510 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9315 (pm20) REVERT: A 533 LEU cc_start: 0.9386 (tp) cc_final: 0.8845 (mt) REVERT: A 656 MET cc_start: 0.9420 (tpt) cc_final: 0.8751 (tpt) REVERT: A 659 GLN cc_start: 0.9444 (mt0) cc_final: 0.9162 (pt0) REVERT: A 697 MET cc_start: 0.8930 (ptm) cc_final: 0.8362 (ptm) REVERT: A 756 MET cc_start: 0.7494 (mtm) cc_final: 0.7101 (mtt) REVERT: A 804 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 816 LEU cc_start: 0.9390 (mt) cc_final: 0.8947 (mm) REVERT: A 817 MET cc_start: 0.8597 (mmp) cc_final: 0.7910 (tpp) REVERT: A 818 PHE cc_start: 0.8701 (m-80) cc_final: 0.8031 (m-80) REVERT: A 854 VAL cc_start: 0.9235 (t) cc_final: 0.8994 (t) REVERT: A 889 ASP cc_start: 0.9143 (m-30) cc_final: 0.8494 (m-30) REVERT: A 901 MET cc_start: 0.8551 (mmp) cc_final: 0.7830 (mmp) REVERT: A 951 THR cc_start: 0.9397 (p) cc_final: 0.9043 (p) REVERT: A 1118 MET cc_start: 0.7556 (ttt) cc_final: 0.6729 (ttt) REVERT: A 1187 MET cc_start: 0.9105 (mtt) cc_final: 0.8833 (mtt) REVERT: A 1190 ASP cc_start: 0.9783 (m-30) cc_final: 0.9417 (p0) REVERT: A 1229 MET cc_start: 0.9676 (ttp) cc_final: 0.9253 (tmm) REVERT: A 1255 PHE cc_start: 0.8127 (m-10) cc_final: 0.7628 (m-80) REVERT: A 1343 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9081 (mm-30) REVERT: B 91 ASP cc_start: 0.9221 (m-30) cc_final: 0.9011 (m-30) REVERT: B 95 ARG cc_start: 0.9317 (ttt180) cc_final: 0.9050 (ttt180) REVERT: B 109 GLU cc_start: 0.8829 (tt0) cc_final: 0.8143 (mp0) REVERT: B 132 ASN cc_start: 0.9137 (m-40) cc_final: 0.8768 (t0) REVERT: B 155 MET cc_start: 0.5150 (ttt) cc_final: 0.4771 (mtp) REVERT: B 157 ILE cc_start: 0.9609 (mt) cc_final: 0.9365 (mm) REVERT: B 259 TYR cc_start: 0.9072 (t80) cc_final: 0.8830 (t80) REVERT: B 283 ARG cc_start: 0.9018 (ptp-170) cc_final: 0.8594 (ptp-170) REVERT: B 291 GLU cc_start: 0.9491 (mt-10) cc_final: 0.8951 (pt0) REVERT: B 295 ARG cc_start: 0.9605 (ptp-110) cc_final: 0.9160 (ptt-90) REVERT: B 467 ASN cc_start: 0.9421 (p0) cc_final: 0.9177 (p0) REVERT: B 561 HIS cc_start: 0.9424 (t-90) cc_final: 0.9211 (t-90) REVERT: B 603 PHE cc_start: 0.9256 (m-80) cc_final: 0.8956 (m-80) REVERT: B 665 LYS cc_start: 0.9272 (tppt) cc_final: 0.8820 (tppt) REVERT: B 756 MET cc_start: 0.8110 (mtt) cc_final: 0.7350 (mtt) REVERT: B 765 LEU cc_start: 0.9466 (tp) cc_final: 0.9256 (tp) REVERT: B 831 PHE cc_start: 0.9000 (p90) cc_final: 0.8748 (p90) REVERT: B 1051 MET cc_start: 0.9358 (ptt) cc_final: 0.8906 (ppp) REVERT: B 1054 MET cc_start: 0.8549 (mmp) cc_final: 0.8049 (mtm) REVERT: B 1118 MET cc_start: 0.8418 (tpp) cc_final: 0.7403 (ttm) REVERT: B 1255 PHE cc_start: 0.8799 (m-80) cc_final: 0.8350 (m-10) REVERT: B 1275 MET cc_start: 0.8513 (ttm) cc_final: 0.7637 (mtm) REVERT: B 1292 LEU cc_start: 0.8469 (pp) cc_final: 0.8239 (pp) outliers start: 2 outliers final: 0 residues processed: 366 average time/residue: 0.1734 time to fit residues: 95.1793 Evaluate side-chains 280 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 239 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 225 optimal weight: 0.4980 chunk 16 optimal weight: 20.0000 chunk 229 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 477 GLN B 811 ASN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 HIS ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.042925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.031830 restraints weight = 160650.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033306 restraints weight = 109436.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.034463 restraints weight = 80246.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.035369 restraints weight = 61942.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036092 restraints weight = 49638.942| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21616 Z= 0.128 Angle : 0.582 9.583 29284 Z= 0.307 Chirality : 0.043 0.202 3302 Planarity : 0.004 0.049 3816 Dihedral : 4.446 22.888 2928 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.09 % Allowed : 2.14 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2714 helix: 1.63 (0.14), residues: 1334 sheet: -0.16 (0.28), residues: 344 loop : 0.05 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.025 0.002 TYR B 841 PHE 0.024 0.002 PHE B 30 TRP 0.014 0.001 TRP A 651 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (21616) covalent geometry : angle 0.58235 / 0.31 (29284) hydrogen bonds : bond 0.03373 / 2.26 ( 1118) hydrogen bonds : angle 4.86092 / 3.41 ( 3246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 0.783 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: A 238 ARG cc_start: 0.8804 (mmp80) cc_final: 0.8599 (mmp80) REVERT: A 256 GLU cc_start: 0.9308 (mp0) cc_final: 0.9072 (mp0) REVERT: A 257 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8798 (mt-10) REVERT: A 287 ILE cc_start: 0.9409 (pt) cc_final: 0.9111 (pt) REVERT: A 291 GLU cc_start: 0.9343 (mp0) cc_final: 0.8958 (mp0) REVERT: A 317 ARG cc_start: 0.9234 (ttp-170) cc_final: 0.8214 (tpt170) REVERT: A 324 ASN cc_start: 0.9520 (m-40) cc_final: 0.9201 (p0) REVERT: A 326 MET cc_start: 0.9486 (ptm) cc_final: 0.9148 (ptm) REVERT: A 510 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9305 (pm20) REVERT: A 533 LEU cc_start: 0.9394 (tp) cc_final: 0.8804 (mt) REVERT: A 654 LEU cc_start: 0.9499 (tt) cc_final: 0.9052 (mt) REVERT: A 656 MET cc_start: 0.9415 (tpt) cc_final: 0.8935 (tpt) REVERT: A 697 MET cc_start: 0.8944 (ptm) cc_final: 0.8385 (ptm) REVERT: A 756 MET cc_start: 0.7314 (mtm) cc_final: 0.6933 (mtt) REVERT: A 804 ILE cc_start: 0.9327 (mp) cc_final: 0.9123 (mp) REVERT: A 816 LEU cc_start: 0.9378 (mt) cc_final: 0.8997 (mm) REVERT: A 817 MET cc_start: 0.8523 (mmp) cc_final: 0.8260 (mmp) REVERT: A 818 PHE cc_start: 0.8690 (m-80) cc_final: 0.7918 (m-80) REVERT: A 854 VAL cc_start: 0.9270 (t) cc_final: 0.9027 (t) REVERT: A 889 ASP cc_start: 0.9190 (m-30) cc_final: 0.8596 (m-30) REVERT: A 901 MET cc_start: 0.8827 (mmp) cc_final: 0.7995 (mmp) REVERT: A 1118 MET cc_start: 0.7571 (ttt) cc_final: 0.6885 (ttt) REVERT: A 1145 THR cc_start: 0.9171 (p) cc_final: 0.8947 (m) REVERT: A 1190 ASP cc_start: 0.9776 (m-30) cc_final: 0.9419 (p0) REVERT: A 1255 PHE cc_start: 0.8137 (m-10) cc_final: 0.7662 (m-80) REVERT: A 1343 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9075 (mm-30) REVERT: B 91 ASP cc_start: 0.9165 (m-30) cc_final: 0.8924 (m-30) REVERT: B 95 ARG cc_start: 0.9261 (ttt180) cc_final: 0.9005 (ttt180) REVERT: B 132 ASN cc_start: 0.9067 (m-40) cc_final: 0.8751 (t0) REVERT: B 157 ILE cc_start: 0.9563 (mt) cc_final: 0.9301 (mm) REVERT: B 259 TYR cc_start: 0.9025 (t80) cc_final: 0.8782 (t80) REVERT: B 291 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9108 (pt0) REVERT: B 295 ARG cc_start: 0.9567 (ptp-110) cc_final: 0.9258 (ptp90) REVERT: B 353 TYR cc_start: 0.8668 (t80) cc_final: 0.8420 (t80) REVERT: B 366 ILE cc_start: 0.9732 (pt) cc_final: 0.9531 (pt) REVERT: B 467 ASN cc_start: 0.9445 (p0) cc_final: 0.9214 (p0) REVERT: B 561 HIS cc_start: 0.9423 (t-90) cc_final: 0.9216 (t-90) REVERT: B 603 PHE cc_start: 0.9229 (m-80) cc_final: 0.8927 (m-80) REVERT: B 656 MET cc_start: 0.9490 (mpp) cc_final: 0.9153 (ptp) REVERT: B 665 LYS cc_start: 0.9272 (tppt) cc_final: 0.8781 (tppt) REVERT: B 742 LEU cc_start: 0.9199 (tt) cc_final: 0.8614 (mp) REVERT: B 754 PHE cc_start: 0.8195 (t80) cc_final: 0.7909 (t80) REVERT: B 756 MET cc_start: 0.8239 (mtt) cc_final: 0.7441 (mtt) REVERT: B 765 LEU cc_start: 0.9430 (tp) cc_final: 0.9103 (tp) REVERT: B 768 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8837 (tp30) REVERT: B 831 PHE cc_start: 0.8879 (p90) cc_final: 0.8358 (p90) REVERT: B 899 MET cc_start: 0.8356 (mmp) cc_final: 0.7968 (mmt) REVERT: B 1051 MET cc_start: 0.9329 (ptt) cc_final: 0.8881 (ppp) REVERT: B 1054 MET cc_start: 0.8433 (mmp) cc_final: 0.7910 (mtm) REVERT: B 1118 MET cc_start: 0.8362 (tpp) cc_final: 0.7329 (ttm) REVERT: B 1205 ASP cc_start: 0.9002 (p0) cc_final: 0.8719 (p0) REVERT: B 1255 PHE cc_start: 0.8850 (m-80) cc_final: 0.8426 (m-80) REVERT: B 1275 MET cc_start: 0.8540 (ttm) cc_final: 0.7788 (mtm) outliers start: 2 outliers final: 0 residues processed: 366 average time/residue: 0.1650 time to fit residues: 91.2692 Evaluate side-chains 285 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 114 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 684 GLN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 HIS B 25 HIS B 477 GLN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN B1059 ASN ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.040253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.029775 restraints weight = 171589.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031146 restraints weight = 117406.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032218 restraints weight = 86587.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033051 restraints weight = 67116.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033722 restraints weight = 54089.523| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 21616 Z= 0.198 Angle : 0.651 8.601 29284 Z= 0.345 Chirality : 0.044 0.259 3302 Planarity : 0.005 0.050 3816 Dihedral : 4.738 21.889 2928 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2714 helix: 1.48 (0.14), residues: 1338 sheet: -0.21 (0.28), residues: 344 loop : -0.01 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 120 TYR 0.023 0.002 TYR B 841 PHE 0.023 0.002 PHE A 762 TRP 0.018 0.002 TRP A 135 HIS 0.008 0.002 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (21616) covalent geometry : angle 0.65124 / 0.34 (29284) hydrogen bonds : bond 0.03786 / 2.56 ( 1118) hydrogen bonds : angle 5.13319 / 3.60 ( 3246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.764 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 170 GLU cc_start: 0.9221 (pt0) cc_final: 0.8916 (tm-30) REVERT: A 256 GLU cc_start: 0.9295 (mp0) cc_final: 0.9073 (mp0) REVERT: A 257 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8766 (mt-10) REVERT: A 317 ARG cc_start: 0.9268 (ttp-170) cc_final: 0.8298 (tpt90) REVERT: A 324 ASN cc_start: 0.9587 (m-40) cc_final: 0.9321 (p0) REVERT: A 510 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9319 (pm20) REVERT: A 533 LEU cc_start: 0.9456 (tp) cc_final: 0.8915 (mt) REVERT: A 539 GLU cc_start: 0.9234 (pt0) cc_final: 0.8750 (tm-30) REVERT: A 583 MET cc_start: 0.8372 (mtp) cc_final: 0.8172 (mtp) REVERT: A 654 LEU cc_start: 0.9538 (tt) cc_final: 0.9189 (mt) REVERT: A 656 MET cc_start: 0.9429 (tpt) cc_final: 0.8796 (tpt) REVERT: A 659 GLN cc_start: 0.9457 (mt0) cc_final: 0.9217 (pt0) REVERT: A 697 MET cc_start: 0.8984 (ptm) cc_final: 0.8476 (ptm) REVERT: A 756 MET cc_start: 0.7369 (mtm) cc_final: 0.7153 (mtt) REVERT: A 816 LEU cc_start: 0.9447 (mt) cc_final: 0.9111 (mm) REVERT: A 817 MET cc_start: 0.8540 (mmp) cc_final: 0.7889 (tpp) REVERT: A 818 PHE cc_start: 0.8721 (m-80) cc_final: 0.7907 (m-80) REVERT: A 854 VAL cc_start: 0.9314 (t) cc_final: 0.9091 (t) REVERT: A 889 ASP cc_start: 0.9225 (m-30) cc_final: 0.8556 (m-30) REVERT: A 899 MET cc_start: 0.8876 (tpp) cc_final: 0.7724 (mmm) REVERT: A 901 MET cc_start: 0.8528 (mmp) cc_final: 0.7562 (mmt) REVERT: A 1187 MET cc_start: 0.9120 (mtt) cc_final: 0.8830 (mtt) REVERT: A 1190 ASP cc_start: 0.9787 (m-30) cc_final: 0.9450 (p0) REVERT: A 1229 MET cc_start: 0.9725 (ttp) cc_final: 0.9454 (mtm) REVERT: A 1235 LEU cc_start: 0.9162 (tp) cc_final: 0.8950 (tt) REVERT: A 1255 PHE cc_start: 0.8229 (m-10) cc_final: 0.7752 (m-80) REVERT: A 1343 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9101 (mm-30) REVERT: B 72 LYS cc_start: 0.9441 (ttpt) cc_final: 0.9195 (ptmt) REVERT: B 95 ARG cc_start: 0.9367 (ttt180) cc_final: 0.9116 (ttt180) REVERT: B 109 GLU cc_start: 0.8688 (pt0) cc_final: 0.8060 (mp0) REVERT: B 132 ASN cc_start: 0.9070 (m-40) cc_final: 0.8728 (t0) REVERT: B 157 ILE cc_start: 0.9636 (mt) cc_final: 0.9407 (mm) REVERT: B 259 TYR cc_start: 0.9091 (t80) cc_final: 0.8864 (t80) REVERT: B 291 GLU cc_start: 0.9489 (mt-10) cc_final: 0.8905 (pt0) REVERT: B 295 ARG cc_start: 0.9598 (ptp-110) cc_final: 0.9099 (ptp90) REVERT: B 467 ASN cc_start: 0.9433 (p0) cc_final: 0.9199 (p0) REVERT: B 603 PHE cc_start: 0.9222 (m-80) cc_final: 0.8921 (m-80) REVERT: B 654 LEU cc_start: 0.9588 (tt) cc_final: 0.9230 (mt) REVERT: B 742 LEU cc_start: 0.9272 (tt) cc_final: 0.8671 (mp) REVERT: B 754 PHE cc_start: 0.8372 (t80) cc_final: 0.7925 (t80) REVERT: B 756 MET cc_start: 0.8391 (mtt) cc_final: 0.7518 (mtt) REVERT: B 822 ASP cc_start: 0.9333 (m-30) cc_final: 0.9118 (m-30) REVERT: B 831 PHE cc_start: 0.9141 (p90) cc_final: 0.8714 (p90) REVERT: B 1051 MET cc_start: 0.9355 (ptt) cc_final: 0.8940 (ptm) REVERT: B 1054 MET cc_start: 0.8556 (mmp) cc_final: 0.8033 (mtt) REVERT: B 1118 MET cc_start: 0.8532 (tpp) cc_final: 0.7390 (ttm) REVERT: B 1229 MET cc_start: 0.8416 (ptp) cc_final: 0.8190 (mtm) REVERT: B 1255 PHE cc_start: 0.8945 (m-80) cc_final: 0.8504 (m-10) REVERT: B 1275 MET cc_start: 0.8703 (ttm) cc_final: 0.7929 (mtm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1685 time to fit residues: 89.0818 Evaluate side-chains 265 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 42 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 160 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 overall best weight: 2.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 ASN ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.041232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.030280 restraints weight = 161703.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031745 restraints weight = 108875.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.032888 restraints weight = 79216.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033790 restraints weight = 60733.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.034501 restraints weight = 48500.719| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21616 Z= 0.140 Angle : 0.601 10.782 29284 Z= 0.314 Chirality : 0.044 0.311 3302 Planarity : 0.004 0.053 3816 Dihedral : 4.514 20.677 2928 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.04 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2714 helix: 1.62 (0.14), residues: 1336 sheet: -0.11 (0.28), residues: 346 loop : 0.05 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 423 TYR 0.018 0.002 TYR A 356 PHE 0.019 0.002 PHE B 30 TRP 0.014 0.002 TRP A 651 HIS 0.005 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (21616) covalent geometry : angle 0.60124 / 0.31 (29284) hydrogen bonds : bond 0.03364 / 2.26 ( 1118) hydrogen bonds : angle 4.95953 / 3.47 ( 3246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.9358 (tttt) cc_final: 0.9123 (tppt) REVERT: A 95 ARG cc_start: 0.9508 (ptt90) cc_final: 0.9283 (ttp80) REVERT: A 183 LYS cc_start: 0.6473 (tttp) cc_final: 0.6095 (tptt) REVERT: A 256 GLU cc_start: 0.9293 (mp0) cc_final: 0.9065 (mp0) REVERT: A 257 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8809 (mt-10) REVERT: A 291 GLU cc_start: 0.9374 (mp0) cc_final: 0.9003 (mp0) REVERT: A 317 ARG cc_start: 0.9245 (ttp-170) cc_final: 0.8336 (tpt170) REVERT: A 324 ASN cc_start: 0.9579 (m-40) cc_final: 0.9340 (p0) REVERT: A 326 MET cc_start: 0.9273 (ptp) cc_final: 0.8993 (ptm) REVERT: A 510 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9303 (pm20) REVERT: A 533 LEU cc_start: 0.9415 (tp) cc_final: 0.8860 (mt) REVERT: A 539 GLU cc_start: 0.9193 (pt0) cc_final: 0.8729 (tm-30) REVERT: A 572 LYS cc_start: 0.9370 (tptt) cc_final: 0.8952 (tptt) REVERT: A 654 LEU cc_start: 0.9537 (tt) cc_final: 0.9136 (mt) REVERT: A 656 MET cc_start: 0.9445 (tpt) cc_final: 0.8800 (tpt) REVERT: A 659 GLN cc_start: 0.9448 (mt0) cc_final: 0.9222 (pt0) REVERT: A 697 MET cc_start: 0.8990 (ptm) cc_final: 0.8435 (ptm) REVERT: A 742 LEU cc_start: 0.9684 (tp) cc_final: 0.9064 (mm) REVERT: A 756 MET cc_start: 0.7168 (mtm) cc_final: 0.6920 (mtt) REVERT: A 799 VAL cc_start: 0.8883 (t) cc_final: 0.8556 (t) REVERT: A 804 ILE cc_start: 0.9296 (mp) cc_final: 0.9036 (mp) REVERT: A 816 LEU cc_start: 0.9442 (mt) cc_final: 0.9166 (mm) REVERT: A 817 MET cc_start: 0.8449 (mmp) cc_final: 0.8196 (mmp) REVERT: A 818 PHE cc_start: 0.8773 (m-80) cc_final: 0.8003 (m-80) REVERT: A 854 VAL cc_start: 0.9332 (t) cc_final: 0.9119 (t) REVERT: A 889 ASP cc_start: 0.9205 (m-30) cc_final: 0.8679 (m-30) REVERT: A 899 MET cc_start: 0.8861 (tpp) cc_final: 0.8146 (mmm) REVERT: A 901 MET cc_start: 0.8365 (mmp) cc_final: 0.7618 (mmt) REVERT: A 1118 MET cc_start: 0.7720 (ttt) cc_final: 0.7515 (ttt) REVERT: A 1190 ASP cc_start: 0.9783 (m-30) cc_final: 0.9445 (p0) REVERT: A 1229 MET cc_start: 0.9737 (ttp) cc_final: 0.9426 (mtm) REVERT: A 1255 PHE cc_start: 0.8191 (m-10) cc_final: 0.7739 (m-80) REVERT: A 1292 LEU cc_start: 0.9373 (pp) cc_final: 0.9137 (mm) REVERT: A 1343 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9072 (mm-30) REVERT: A 1382 TYR cc_start: 0.7807 (p90) cc_final: 0.7438 (p90) REVERT: A 1391 MET cc_start: 0.8090 (ppp) cc_final: 0.7734 (ppp) REVERT: B 72 LYS cc_start: 0.9439 (ttpt) cc_final: 0.9211 (ptmt) REVERT: B 109 GLU cc_start: 0.8727 (pt0) cc_final: 0.8028 (mp0) REVERT: B 112 LEU cc_start: 0.9129 (tp) cc_final: 0.8601 (tt) REVERT: B 132 ASN cc_start: 0.9065 (m-40) cc_final: 0.8743 (t0) REVERT: B 157 ILE cc_start: 0.9622 (mt) cc_final: 0.9379 (mm) REVERT: B 256 GLU cc_start: 0.9346 (mp0) cc_final: 0.8929 (mp0) REVERT: B 259 TYR cc_start: 0.9067 (t80) cc_final: 0.8826 (t80) REVERT: B 291 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8842 (pt0) REVERT: B 295 ARG cc_start: 0.9568 (ptp-110) cc_final: 0.9093 (ptp90) REVERT: B 338 THR cc_start: 0.8576 (t) cc_final: 0.8217 (p) REVERT: B 366 ILE cc_start: 0.9709 (pt) cc_final: 0.9439 (pt) REVERT: B 467 ASN cc_start: 0.9438 (p0) cc_final: 0.9210 (p0) REVERT: B 542 MET cc_start: 0.9666 (tmm) cc_final: 0.9463 (tmm) REVERT: B 603 PHE cc_start: 0.9209 (m-80) cc_final: 0.8898 (m-80) REVERT: B 654 LEU cc_start: 0.9497 (tt) cc_final: 0.9180 (mt) REVERT: B 742 LEU cc_start: 0.9303 (tt) cc_final: 0.8692 (mp) REVERT: B 754 PHE cc_start: 0.8318 (t80) cc_final: 0.7750 (t80) REVERT: B 756 MET cc_start: 0.8251 (mtt) cc_final: 0.7409 (mtt) REVERT: B 765 LEU cc_start: 0.9475 (tp) cc_final: 0.9263 (tp) REVERT: B 773 LYS cc_start: 0.9215 (tptt) cc_final: 0.8899 (tppt) REVERT: B 831 PHE cc_start: 0.8995 (p90) cc_final: 0.8580 (p90) REVERT: B 976 THR cc_start: 0.9574 (m) cc_final: 0.9336 (t) REVERT: B 1051 MET cc_start: 0.9294 (ptt) cc_final: 0.8840 (ptt) REVERT: B 1054 MET cc_start: 0.8238 (mmp) cc_final: 0.7910 (mtt) REVERT: B 1118 MET cc_start: 0.8501 (tpp) cc_final: 0.7334 (ttm) REVERT: B 1210 MET cc_start: 0.8277 (mmp) cc_final: 0.6621 (tmm) REVERT: B 1255 PHE cc_start: 0.8939 (m-80) cc_final: 0.8497 (m-10) REVERT: B 1275 MET cc_start: 0.8634 (ttm) cc_final: 0.7738 (mtm) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1612 time to fit residues: 87.4034 Evaluate side-chains 268 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.039685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029190 restraints weight = 169518.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.030596 restraints weight = 113882.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.031674 restraints weight = 82925.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032535 restraints weight = 63908.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033205 restraints weight = 51108.704| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 21616 Z= 0.191 Angle : 0.651 9.760 29284 Z= 0.342 Chirality : 0.044 0.268 3302 Planarity : 0.005 0.112 3816 Dihedral : 4.713 21.780 2928 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2714 helix: 1.56 (0.14), residues: 1324 sheet: -0.27 (0.28), residues: 346 loop : -0.02 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1168 TYR 0.019 0.002 TYR B 868 PHE 0.026 0.002 PHE A 762 TRP 0.015 0.002 TRP A 651 HIS 0.007 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (21616) covalent geometry : angle 0.65136 / 0.34 (29284) hydrogen bonds : bond 0.03693 / 2.49 ( 1118) hydrogen bonds : angle 5.13959 / 3.60 ( 3246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.802 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 159 TYR cc_start: 0.8753 (m-10) cc_final: 0.8389 (m-10) REVERT: A 170 GLU cc_start: 0.9232 (pt0) cc_final: 0.8933 (tm-30) REVERT: A 256 GLU cc_start: 0.9343 (mp0) cc_final: 0.8957 (pm20) REVERT: A 287 ILE cc_start: 0.9313 (pt) cc_final: 0.9068 (pt) REVERT: A 291 GLU cc_start: 0.9382 (mp0) cc_final: 0.9028 (mp0) REVERT: A 317 ARG cc_start: 0.9258 (ttp-170) cc_final: 0.8332 (tpt170) REVERT: A 324 ASN cc_start: 0.9619 (m-40) cc_final: 0.9409 (p0) REVERT: A 326 MET cc_start: 0.9261 (ptp) cc_final: 0.8970 (ptm) REVERT: A 510 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9318 (pm20) REVERT: A 533 LEU cc_start: 0.9450 (tp) cc_final: 0.8897 (mt) REVERT: A 539 GLU cc_start: 0.9246 (pt0) cc_final: 0.8781 (tm-30) REVERT: A 583 MET cc_start: 0.8440 (mtp) cc_final: 0.8216 (mtp) REVERT: A 654 LEU cc_start: 0.9538 (tt) cc_final: 0.9157 (mt) REVERT: A 656 MET cc_start: 0.9410 (tpt) cc_final: 0.8792 (tpt) REVERT: A 697 MET cc_start: 0.9001 (ptm) cc_final: 0.8460 (ptm) REVERT: A 816 LEU cc_start: 0.9510 (mt) cc_final: 0.9216 (mm) REVERT: A 817 MET cc_start: 0.8460 (mmp) cc_final: 0.7814 (tpp) REVERT: A 818 PHE cc_start: 0.8713 (m-80) cc_final: 0.7889 (m-80) REVERT: A 889 ASP cc_start: 0.9180 (m-30) cc_final: 0.8524 (m-30) REVERT: A 899 MET cc_start: 0.8823 (tpp) cc_final: 0.8169 (mmm) REVERT: A 901 MET cc_start: 0.8188 (mmp) cc_final: 0.7189 (mmt) REVERT: A 951 THR cc_start: 0.9527 (p) cc_final: 0.9248 (p) REVERT: A 1187 MET cc_start: 0.9115 (mtt) cc_final: 0.8826 (mtt) REVERT: A 1190 ASP cc_start: 0.9784 (m-30) cc_final: 0.9467 (p0) REVERT: A 1229 MET cc_start: 0.9736 (ttp) cc_final: 0.9410 (mtm) REVERT: A 1255 PHE cc_start: 0.8189 (m-10) cc_final: 0.7720 (m-80) REVERT: A 1343 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9155 (mm-30) REVERT: A 1385 ASN cc_start: 0.9342 (m110) cc_final: 0.9013 (m110) REVERT: B 132 ASN cc_start: 0.9076 (m-40) cc_final: 0.8784 (t0) REVERT: B 152 GLU cc_start: 0.9104 (pt0) cc_final: 0.8890 (pp20) REVERT: B 155 MET cc_start: 0.5205 (tpt) cc_final: 0.4432 (tpp) REVERT: B 157 ILE cc_start: 0.9597 (mt) cc_final: 0.9322 (mm) REVERT: B 256 GLU cc_start: 0.9352 (mp0) cc_final: 0.8960 (mp0) REVERT: B 259 TYR cc_start: 0.9098 (t80) cc_final: 0.8869 (t80) REVERT: B 291 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8981 (pt0) REVERT: B 295 ARG cc_start: 0.9570 (ptp-110) cc_final: 0.9113 (ptp90) REVERT: B 467 ASN cc_start: 0.9469 (p0) cc_final: 0.9249 (p0) REVERT: B 542 MET cc_start: 0.9630 (tmm) cc_final: 0.9394 (tmm) REVERT: B 603 PHE cc_start: 0.9186 (m-80) cc_final: 0.8879 (m-80) REVERT: B 654 LEU cc_start: 0.9567 (tt) cc_final: 0.9295 (mt) REVERT: B 742 LEU cc_start: 0.9290 (tt) cc_final: 0.8641 (mp) REVERT: B 754 PHE cc_start: 0.8447 (t80) cc_final: 0.7873 (t80) REVERT: B 756 MET cc_start: 0.8241 (mtt) cc_final: 0.7294 (mtt) REVERT: B 773 LYS cc_start: 0.9236 (tptt) cc_final: 0.8672 (tppt) REVERT: B 822 ASP cc_start: 0.9324 (m-30) cc_final: 0.8434 (t70) REVERT: B 831 PHE cc_start: 0.9133 (p90) cc_final: 0.8865 (p90) REVERT: B 976 THR cc_start: 0.9596 (m) cc_final: 0.9364 (t) REVERT: B 1051 MET cc_start: 0.9304 (ptt) cc_final: 0.8865 (ptm) REVERT: B 1054 MET cc_start: 0.8339 (mmp) cc_final: 0.8048 (mtt) REVERT: B 1118 MET cc_start: 0.8481 (tpp) cc_final: 0.7278 (ttm) REVERT: B 1255 PHE cc_start: 0.8939 (m-80) cc_final: 0.8486 (m-10) REVERT: B 1275 MET cc_start: 0.8688 (ttm) cc_final: 0.7919 (mtt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1641 time to fit residues: 86.4081 Evaluate side-chains 259 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 101 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 88 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 ASN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN B 477 GLN ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.039354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.028794 restraints weight = 168999.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.030196 restraints weight = 113621.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031291 restraints weight = 82777.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.032154 restraints weight = 63595.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032837 restraints weight = 50831.671| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21616 Z= 0.191 Angle : 0.663 9.236 29284 Z= 0.348 Chirality : 0.045 0.331 3302 Planarity : 0.005 0.062 3816 Dihedral : 4.795 21.492 2928 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2714 helix: 1.42 (0.14), residues: 1338 sheet: -0.39 (0.28), residues: 350 loop : -0.06 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 313 TYR 0.030 0.002 TYR B1227 PHE 0.026 0.002 PHE A 762 TRP 0.028 0.002 TRP B 135 HIS 0.007 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (21616) covalent geometry : angle 0.66282 / 0.35 (29284) hydrogen bonds : bond 0.03719 / 2.50 ( 1118) hydrogen bonds : angle 5.20912 / 3.64 ( 3246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9249 (mppt) cc_final: 0.8907 (mmtm) REVERT: A 170 GLU cc_start: 0.9230 (pt0) cc_final: 0.8856 (tm-30) REVERT: A 287 ILE cc_start: 0.9312 (pt) cc_final: 0.9065 (pt) REVERT: A 291 GLU cc_start: 0.9316 (mp0) cc_final: 0.8957 (mp0) REVERT: A 510 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9311 (pm20) REVERT: A 539 GLU cc_start: 0.9184 (pt0) cc_final: 0.8670 (tm-30) REVERT: A 583 MET cc_start: 0.8422 (mtp) cc_final: 0.8220 (mtp) REVERT: A 654 LEU cc_start: 0.9575 (tt) cc_final: 0.9202 (mt) REVERT: A 656 MET cc_start: 0.9259 (tpt) cc_final: 0.8919 (tpt) REVERT: A 659 GLN cc_start: 0.9544 (pt0) cc_final: 0.9322 (mm-40) REVERT: A 676 MET cc_start: 0.9338 (pmm) cc_final: 0.9117 (pmm) REVERT: A 697 MET cc_start: 0.8967 (ptm) cc_final: 0.8446 (ptm) REVERT: A 816 LEU cc_start: 0.9521 (mt) cc_final: 0.9239 (mm) REVERT: A 817 MET cc_start: 0.8463 (mmp) cc_final: 0.7831 (tpp) REVERT: A 818 PHE cc_start: 0.8693 (m-80) cc_final: 0.7896 (m-80) REVERT: A 853 MET cc_start: 0.8749 (pmm) cc_final: 0.8190 (ppp) REVERT: A 889 ASP cc_start: 0.9166 (m-30) cc_final: 0.8495 (m-30) REVERT: A 901 MET cc_start: 0.8118 (mmp) cc_final: 0.7010 (mmt) REVERT: A 937 MET cc_start: 0.8618 (ttm) cc_final: 0.8248 (tpp) REVERT: A 1118 MET cc_start: 0.7670 (ttt) cc_final: 0.7413 (ttt) REVERT: A 1190 ASP cc_start: 0.9794 (m-30) cc_final: 0.9501 (p0) REVERT: A 1215 VAL cc_start: 0.9427 (m) cc_final: 0.9110 (p) REVERT: A 1229 MET cc_start: 0.9732 (ttp) cc_final: 0.9420 (mtm) REVERT: A 1286 LEU cc_start: 0.9667 (mt) cc_final: 0.9448 (mt) REVERT: A 1343 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9146 (mm-30) REVERT: B 132 ASN cc_start: 0.9054 (m-40) cc_final: 0.8754 (t0) REVERT: B 152 GLU cc_start: 0.9114 (pt0) cc_final: 0.8896 (pp20) REVERT: B 155 MET cc_start: 0.5303 (tpt) cc_final: 0.4425 (tpp) REVERT: B 157 ILE cc_start: 0.9593 (mt) cc_final: 0.9350 (mm) REVERT: B 256 GLU cc_start: 0.9332 (mp0) cc_final: 0.8935 (mp0) REVERT: B 259 TYR cc_start: 0.9087 (t80) cc_final: 0.8879 (t80) REVERT: B 291 GLU cc_start: 0.9489 (mt-10) cc_final: 0.8995 (pt0) REVERT: B 295 ARG cc_start: 0.9589 (ptp-110) cc_final: 0.9143 (ptp90) REVERT: B 363 ILE cc_start: 0.9182 (mm) cc_final: 0.8859 (mm) REVERT: B 467 ASN cc_start: 0.9484 (p0) cc_final: 0.9282 (p0) REVERT: B 603 PHE cc_start: 0.9170 (m-80) cc_final: 0.8856 (m-80) REVERT: B 654 LEU cc_start: 0.9640 (tt) cc_final: 0.9309 (mt) REVERT: B 742 LEU cc_start: 0.9363 (tt) cc_final: 0.8700 (mp) REVERT: B 754 PHE cc_start: 0.8476 (t80) cc_final: 0.7895 (t80) REVERT: B 756 MET cc_start: 0.8123 (mtt) cc_final: 0.7188 (mtt) REVERT: B 773 LYS cc_start: 0.9244 (tptt) cc_final: 0.8671 (tppt) REVERT: B 822 ASP cc_start: 0.9319 (m-30) cc_final: 0.8455 (t70) REVERT: B 831 PHE cc_start: 0.9113 (p90) cc_final: 0.8850 (p90) REVERT: B 899 MET cc_start: 0.7944 (mmp) cc_final: 0.7630 (mmm) REVERT: B 976 THR cc_start: 0.9602 (m) cc_final: 0.9365 (t) REVERT: B 1051 MET cc_start: 0.9300 (ptt) cc_final: 0.8828 (ptm) REVERT: B 1054 MET cc_start: 0.8366 (mmp) cc_final: 0.7895 (mtp) REVERT: B 1059 ASN cc_start: 0.9490 (m110) cc_final: 0.9287 (m-40) REVERT: B 1176 ASN cc_start: 0.9277 (m-40) cc_final: 0.8992 (t0) REVERT: B 1210 MET cc_start: 0.8318 (mmp) cc_final: 0.6678 (tmm) REVERT: B 1255 PHE cc_start: 0.8961 (m-80) cc_final: 0.8524 (m-10) REVERT: B 1275 MET cc_start: 0.8715 (ttm) cc_final: 0.8106 (mtt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1650 time to fit residues: 85.1363 Evaluate side-chains 260 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 GLN A1297 ASN B 39 GLN B 477 GLN ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.039552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029040 restraints weight = 170396.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.030423 restraints weight = 115648.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031490 restraints weight = 84618.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032338 restraints weight = 65366.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.032998 restraints weight = 52472.668| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.7812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21616 Z= 0.180 Angle : 0.663 9.353 29284 Z= 0.348 Chirality : 0.045 0.316 3302 Planarity : 0.005 0.062 3816 Dihedral : 4.832 27.893 2928 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2714 helix: 1.39 (0.14), residues: 1340 sheet: -0.27 (0.28), residues: 346 loop : -0.10 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1168 TYR 0.030 0.002 TYR B1227 PHE 0.026 0.002 PHE A 762 TRP 0.019 0.002 TRP B 135 HIS 0.007 0.001 HIS B1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (21616) covalent geometry : angle 0.66272 / 0.35 (29284) hydrogen bonds : bond 0.03670 / 2.46 ( 1118) hydrogen bonds : angle 5.22023 / 3.65 ( 3246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.794 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: A 170 GLU cc_start: 0.9178 (pt0) cc_final: 0.8852 (tm-30) REVERT: A 256 GLU cc_start: 0.9432 (mp0) cc_final: 0.9201 (mp0) REVERT: A 287 ILE cc_start: 0.9299 (pt) cc_final: 0.9074 (pt) REVERT: A 291 GLU cc_start: 0.9320 (mp0) cc_final: 0.9011 (mp0) REVERT: A 317 ARG cc_start: 0.9279 (ttp-170) cc_final: 0.8357 (tpt170) REVERT: A 510 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9315 (pm20) REVERT: A 539 GLU cc_start: 0.9215 (pt0) cc_final: 0.8645 (tm-30) REVERT: A 654 LEU cc_start: 0.9589 (tt) cc_final: 0.9194 (mt) REVERT: A 656 MET cc_start: 0.9269 (tpt) cc_final: 0.8800 (tpt) REVERT: A 676 MET cc_start: 0.9356 (pmm) cc_final: 0.9149 (pmm) REVERT: A 697 MET cc_start: 0.9018 (ptm) cc_final: 0.8482 (ptm) REVERT: A 816 LEU cc_start: 0.9527 (mt) cc_final: 0.9259 (mm) REVERT: A 817 MET cc_start: 0.8453 (mmp) cc_final: 0.8077 (mmp) REVERT: A 818 PHE cc_start: 0.8723 (m-80) cc_final: 0.7971 (m-80) REVERT: A 853 MET cc_start: 0.8785 (pmm) cc_final: 0.8181 (ppp) REVERT: A 889 ASP cc_start: 0.9172 (m-30) cc_final: 0.8541 (m-30) REVERT: A 901 MET cc_start: 0.8069 (mmp) cc_final: 0.7056 (mmt) REVERT: A 951 THR cc_start: 0.9548 (p) cc_final: 0.9272 (p) REVERT: A 954 LYS cc_start: 0.9529 (tptp) cc_final: 0.9294 (ptpp) REVERT: A 1190 ASP cc_start: 0.9798 (m-30) cc_final: 0.9508 (p0) REVERT: A 1215 VAL cc_start: 0.9461 (m) cc_final: 0.9201 (p) REVERT: A 1229 MET cc_start: 0.9729 (ttp) cc_final: 0.9381 (mtm) REVERT: A 1343 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9109 (mm-30) REVERT: B 111 GLU cc_start: 0.8838 (tt0) cc_final: 0.7097 (tt0) REVERT: B 132 ASN cc_start: 0.9114 (m-40) cc_final: 0.8801 (t0) REVERT: B 155 MET cc_start: 0.5205 (tpt) cc_final: 0.4288 (tpp) REVERT: B 157 ILE cc_start: 0.9608 (mt) cc_final: 0.9365 (mm) REVERT: B 256 GLU cc_start: 0.9309 (mp0) cc_final: 0.8903 (mp0) REVERT: B 259 TYR cc_start: 0.9068 (t80) cc_final: 0.8850 (t80) REVERT: B 363 ILE cc_start: 0.9144 (mm) cc_final: 0.8821 (mm) REVERT: B 467 ASN cc_start: 0.9500 (p0) cc_final: 0.9298 (p0) REVERT: B 542 MET cc_start: 0.9692 (tmm) cc_final: 0.9485 (tmm) REVERT: B 603 PHE cc_start: 0.9146 (m-80) cc_final: 0.8828 (m-80) REVERT: B 665 LYS cc_start: 0.9235 (tppt) cc_final: 0.8880 (tppt) REVERT: B 742 LEU cc_start: 0.9373 (tt) cc_final: 0.8703 (mp) REVERT: B 754 PHE cc_start: 0.8491 (t80) cc_final: 0.7861 (t80) REVERT: B 756 MET cc_start: 0.8094 (mtt) cc_final: 0.7178 (mtt) REVERT: B 773 LYS cc_start: 0.9259 (tptt) cc_final: 0.8693 (tppt) REVERT: B 822 ASP cc_start: 0.9283 (m-30) cc_final: 0.8457 (t70) REVERT: B 831 PHE cc_start: 0.8966 (p90) cc_final: 0.8700 (p90) REVERT: B 976 THR cc_start: 0.9610 (m) cc_final: 0.9370 (t) REVERT: B 1001 TYR cc_start: 0.8160 (m-80) cc_final: 0.7871 (m-80) REVERT: B 1051 MET cc_start: 0.9294 (ptt) cc_final: 0.8779 (ptt) REVERT: B 1054 MET cc_start: 0.8264 (mmp) cc_final: 0.7897 (mtp) REVERT: B 1059 ASN cc_start: 0.9489 (m110) cc_final: 0.9287 (m-40) REVERT: B 1176 ASN cc_start: 0.9279 (m-40) cc_final: 0.9035 (t0) REVERT: B 1255 PHE cc_start: 0.8958 (m-80) cc_final: 0.8621 (m-10) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1668 time to fit residues: 85.1822 Evaluate side-chains 254 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 44 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 224 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 652 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 310 HIS ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 GLN ** B1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.041631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030460 restraints weight = 163452.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.031936 restraints weight = 110075.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033094 restraints weight = 80275.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034006 restraints weight = 61781.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.034735 restraints weight = 49438.344| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21616 Z= 0.129 Angle : 0.640 11.906 29284 Z= 0.329 Chirality : 0.045 0.299 3302 Planarity : 0.004 0.056 3816 Dihedral : 4.609 26.198 2928 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2714 helix: 1.58 (0.14), residues: 1342 sheet: -0.14 (0.28), residues: 350 loop : -0.02 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 283 TYR 0.026 0.002 TYR B1227 PHE 0.023 0.002 PHE A 762 TRP 0.014 0.002 TRP B 135 HIS 0.008 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21616) covalent geometry : angle 0.63979 / 0.33 (29284) hydrogen bonds : bond 0.03349 / 2.24 ( 1118) hydrogen bonds : angle 4.97678 / 3.50 ( 3246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.36 seconds wall clock time: 68 minutes 1.78 seconds (4081.78 seconds total)