Starting phenix.real_space_refine on Fri Feb 6 01:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392.map" model { file = "/net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkm_62392/02_2026/9kkm_62392_neut.cif" } resolution = 4.14 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= -0.026 sd= 0.797 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 88 5.16 5 C 13452 2.51 5 N 3686 2.21 5 O 4022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21254 Number of models: 1 Model: "" Number of chains: 4 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 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.89, per 1000 atoms: 0.23 Number of scatterers: 21254 At special positions: 0 Unit cell: (122.858, 188.208, 121.551, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Mg 2 11.99 O 4022 8.00 N 3686 7.00 C 13452 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: 1.58 Conformation dependent library (CDL) restraints added in 933.3 milliseconds 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: 1.03 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: 3.814A 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: 3.707A 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: 3.546A 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: 3.978A pdb=" N ASN A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 3.987A pdb=" N GLU A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 5.603A 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: 3.663A 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: 7.735A 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: 3.569A 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: 4.338A 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: 3.809A 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: 3.998A 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: 3.507A 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: 3.540A 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: 4.551A pdb=" N ARG B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.655A 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: 3.745A 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: 3.740A 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: 4.274A 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: 3.511A 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: 4.431A 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: 3.680A 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: 3.665A pdb=" N THR B 976 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.603A 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: 3.654A 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: 3.776A 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: 4.733A 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: 4.718A 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: 8.294A 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: 7.795A 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: 7.861A pdb=" N ASP A 162 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN A 126 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 163 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA A 202 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 5.854A 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: 8.038A 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: 4.733A 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: 4.718A 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: 8.294A 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: 7.795A 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: 7.861A pdb=" N ASP A 162 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN A 126 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 163 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.152A 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: 8.108A 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: 7.487A 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: 8.144A 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: 4.226A 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: 6.965A 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: 6.663A pdb=" N CYS A 778 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A 820 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 5.875A 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: 6.392A 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: 7.899A pdb=" N VAL A 880 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 6.253A 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: 4.214A pdb=" N VAL A 969 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 942 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 8.029A 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: 5.890A pdb=" N VAL A1226 " --> pdb=" O ASN A1220 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN A1220 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 5.414A 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: 12.968A pdb=" N LEU A1147 " --> pdb=" O VAL A1172 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL A1172 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS A1149 " --> pdb=" O CYS A1170 " (cutoff:3.500A) removed outlier: 4.154A 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: 6.329A 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: 10.819A pdb=" N THR A1280 " --> pdb=" O GLN A1177 " (cutoff:3.500A) removed outlier: 6.547A 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: 6.446A pdb=" N GLY B 197 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.938A 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: 7.077A 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: 6.021A 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: 6.464A 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: 7.265A 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: 6.045A pdb=" N MET B 817 " --> pdb=" O TYR B 840 " (cutoff:3.500A) removed outlier: 7.473A 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: 8.283A pdb=" N VAL B 880 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 6.536A 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: 6.393A 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: 7.867A 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: 5.449A pdb=" N PHE B1228 " --> pdb=" O ILE B1218 " (cutoff:3.500A) removed outlier: 6.077A 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: 7.110A 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: 4.738A pdb=" N LEU B1167 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 6.538A 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: 13.870A 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: 4.86 Time building geometry restraints manager: 2.21 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: 4867 1.34 - 1.46: 5210 1.46 - 1.58: 11441 1.58 - 1.70: 6 1.70 - 1.83: 150 Bond restraints: 21674 Sorted by residual: bond pdb=" C4 ADP A1601 " pdb=" C5 ADP A1601 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C4 ADP B1601 " pdb=" C5 ADP B1601 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C5 ADP A1601 " pdb=" C6 ADP A1601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 ADP B1601 " pdb=" C6 ADP B1601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CA LYS B 938 " pdb=" C LYS B 938 " ideal model delta sigma weight residual 1.518 1.552 -0.034 9.60e-03 1.09e+04 1.28e+01 ... (remaining 21669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.51: 29280 6.51 - 13.02: 92 13.02 - 19.52: 0 19.52 - 26.03: 1 26.03 - 32.54: 1 Bond angle restraints: 29374 Sorted by residual: angle pdb=" C GLU A1141 " pdb=" CA GLU A1141 " pdb=" CB GLU A1141 " ideal model delta sigma weight residual 110.07 77.53 32.54 2.20e+00 2.07e-01 2.19e+02 angle pdb=" N LEU B1097 " pdb=" CA LEU B1097 " pdb=" CB LEU B1097 " ideal model delta sigma weight residual 110.83 136.55 -25.72 1.74e+00 3.30e-01 2.18e+02 angle pdb=" CA ASP B 972 " pdb=" CB ASP B 972 " pdb=" CG ASP B 972 " ideal model delta sigma weight residual 112.60 121.79 -9.19 1.00e+00 1.00e+00 8.45e+01 angle pdb=" CA ASP A1287 " pdb=" CB ASP A1287 " pdb=" CG ASP A1287 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.19e+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 ... (remaining 29369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 12741 29.37 - 58.73: 250 58.73 - 88.10: 112 88.10 - 117.47: 8 117.47 - 146.84: 3 Dihedral angle restraints: 13114 sinusoidal: 5216 harmonic: 7898 Sorted by residual: dihedral pdb=" N LEU B1097 " pdb=" C LEU B1097 " pdb=" CA LEU B1097 " pdb=" CB LEU B1097 " ideal model delta harmonic sigma weight residual 122.80 163.46 -40.66 0 2.50e+00 1.60e-01 2.65e+02 dihedral pdb=" C GLU A1141 " pdb=" N GLU A1141 " pdb=" CA GLU A1141 " pdb=" CB GLU A1141 " ideal model delta harmonic sigma weight residual -122.60 -83.32 -39.28 0 2.50e+00 1.60e-01 2.47e+02 dihedral pdb=" C LEU B1097 " pdb=" N LEU B1097 " pdb=" CA LEU B1097 " pdb=" CB LEU B1097 " ideal model delta harmonic sigma weight residual -122.60 -157.28 34.68 0 2.50e+00 1.60e-01 1.92e+02 ... (remaining 13111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 3286 0.329 - 0.658: 22 0.658 - 0.987: 1 0.987 - 1.317: 0 1.317 - 1.646: 1 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA LEU B1097 " pdb=" N LEU B1097 " pdb=" C LEU B1097 " pdb=" CB LEU B1097 " both_signs ideal model delta sigma weight residual False 2.51 0.86 1.65 2.00e-01 2.50e+01 6.77e+01 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 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU A1141 " pdb=" N GLU A1141 " pdb=" C GLU A1141 " pdb=" CB GLU A1141 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.16e+00 ... (remaining 3307 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.108 2.00e-02 2.50e+03 6.24e-02 7.79e+01 pdb=" CG TYR A 351 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.040 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 6.59e-02 7.59e+01 pdb=" CG PHE B 522 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE B 522 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE B 522 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE B 522 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 522 " 0.021 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 6.48e-02 7.35e+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 3815 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 18 2.47 - 3.08: 10513 3.08 - 3.69: 33143 3.69 - 4.29: 49855 4.29 - 4.90: 81910 Nonbonded interactions: 175439 Sorted by model distance: nonbonded pdb=" O3A ADP A1601 " pdb="MG MG A1602 " model vdw 1.864 2.170 nonbonded pdb=" O1B ADP B1601 " pdb="MG MG B1602 " model vdw 2.166 2.170 nonbonded pdb=" OE2 GLU B1230 " pdb=" O1A ADP B1601 " model vdw 2.243 3.040 nonbonded pdb=" CZ PHE A 762 " pdb=" CD1 ILE A 804 " model vdw 2.246 3.760 nonbonded pdb=" CE1 PHE A 762 " pdb=" CD1 LEU A 766 " model vdw 2.258 3.760 ... (remaining 175434 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: 0.04 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.330 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.108 21674 Z= 0.896 Angle : 2.022 32.539 29374 Z= 1.423 Chirality : 0.114 1.646 3310 Planarity : 0.012 0.099 3818 Dihedral : 14.948 146.837 8018 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.74 % Allowed : 2.79 % Favored : 96.47 % Cbeta Deviations : 0.39 % 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: -1.44 (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 0.035 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 covalent geometry : bond 0.01494 (21674) covalent geometry : angle 2.02177 (29374) hydrogen bonds : bond 0.21914 ( 1118) hydrogen bonds : angle 8.29807 ( 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 481 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 464 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 TYR cc_start: 0.9095 (m-80) cc_final: 0.8479 (m-80) REVERT: A 225 PHE cc_start: 0.8719 (t80) cc_final: 0.8353 (t80) REVERT: A 257 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8961 (mt-10) REVERT: A 726 THR cc_start: 0.8248 (p) cc_final: 0.7629 (p) REVERT: A 754 PHE cc_start: 0.8280 (t80) cc_final: 0.8039 (t80) REVERT: A 756 MET cc_start: 0.6925 (mtm) cc_final: 0.6608 (mtm) REVERT: A 822 ASP cc_start: 0.9182 (m-30) cc_final: 0.8381 (t70) REVERT: A 955 LEU cc_start: 0.9483 (mt) cc_final: 0.9259 (tp) REVERT: A 1118 MET cc_start: 0.5918 (tpp) cc_final: 0.5378 (tpp) REVERT: A 1200 THR cc_start: 0.8278 (m) cc_final: 0.8059 (p) REVERT: A 1215 VAL cc_start: 0.9500 (m) cc_final: 0.8931 (t) REVERT: A 1231 MET cc_start: 0.7838 (ttt) cc_final: 0.7076 (tpt) REVERT: B 18 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8299 (Cg_endo) REVERT: B 167 ASP cc_start: 0.5335 (t0) cc_final: 0.5016 (p0) REVERT: B 196 VAL cc_start: 0.9400 (t) cc_final: 0.9019 (p) REVERT: B 259 TYR cc_start: 0.7347 (t80) cc_final: 0.7066 (t80) REVERT: B 283 ARG cc_start: 0.9512 (ttt180) cc_final: 0.9304 (ttt180) REVERT: B 605 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7795 (mm-40) REVERT: B 653 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8047 (mmm160) REVERT: B 692 ILE cc_start: 0.8406 (mm) cc_final: 0.8082 (mm) REVERT: B 709 LEU cc_start: 0.9704 (mt) cc_final: 0.9384 (pp) REVERT: B 724 LEU cc_start: 0.8800 (tp) cc_final: 0.8583 (tp) REVERT: B 730 ASP cc_start: 0.5361 (OUTLIER) cc_final: 0.5040 (m-30) REVERT: B 746 ASN cc_start: 0.4988 (t0) cc_final: 0.4629 (t0) REVERT: B 812 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8486 (mm-30) REVERT: B 820 PHE cc_start: 0.7189 (p90) cc_final: 0.6782 (p90) REVERT: B 822 ASP cc_start: 0.9510 (m-30) cc_final: 0.8985 (p0) REVERT: B 901 MET cc_start: 0.6868 (mmp) cc_final: 0.6633 (tpp) REVERT: B 927 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8859 (tm-30) REVERT: B 975 MET cc_start: 0.9033 (mmm) cc_final: 0.8784 (mmm) REVERT: B 1025 PHE cc_start: 0.8402 (m-10) cc_final: 0.7527 (m-10) REVERT: B 1083 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9472 (tp30) REVERT: B 1239 HIS cc_start: 0.8587 (p-80) cc_final: 0.8194 (m170) REVERT: B 1305 VAL cc_start: 0.7387 (t) cc_final: 0.6765 (p) REVERT: B 1306 PHE cc_start: 0.7379 (m-80) cc_final: 0.7156 (m-80) REVERT: B 1385 ASN cc_start: 0.8724 (m-40) cc_final: 0.8390 (t0) outliers start: 17 outliers final: 2 residues processed: 481 average time/residue: 0.1877 time to fit residues: 128.2999 Evaluate side-chains 262 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 258 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 175 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 470 ASN A 528 ASN A 561 HIS A 659 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS A1042 ASN A1153 GLN A1254 GLN ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 HIS B 175 GLN B 389 GLN B 390 GLN B 462 HIS B 470 ASN B 477 GLN B 528 ASN B 553 ASN B 585 GLN B 684 GLN B 811 ASN B 852 GLN ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 HIS B1049 HIS B1076 HIS B1293 GLN B1309 HIS B1350 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.042814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.034461 restraints weight = 208920.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.035652 restraints weight = 144841.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.036557 restraints weight = 107181.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.037276 restraints weight = 83313.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.037848 restraints weight = 66867.571| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 21674 Z= 0.203 Angle : 0.715 13.322 29374 Z= 0.372 Chirality : 0.045 0.211 3310 Planarity : 0.005 0.052 3818 Dihedral : 6.835 117.098 2950 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 0.17 % Allowed : 2.31 % Favored : 97.51 % 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: 0.11 (0.16), residues: 2714 helix: 0.58 (0.13), residues: 1370 sheet: -0.71 (0.26), residues: 362 loop : -0.11 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1174 TYR 0.024 0.002 TYR A 353 PHE 0.022 0.002 PHE A 300 TRP 0.015 0.002 TRP A 598 HIS 0.006 0.002 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00427 (21674) covalent geometry : angle 0.71549 (29374) hydrogen bonds : bond 0.04433 ( 1118) hydrogen bonds : angle 5.33531 ( 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 255 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.561 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: A 45 ILE cc_start: 0.8836 (mp) cc_final: 0.8352 (mp) REVERT: A 58 LEU cc_start: 0.9446 (mt) cc_final: 0.9226 (mt) REVERT: A 141 TYR cc_start: 0.8936 (m-80) cc_final: 0.8281 (m-80) REVERT: A 676 MET cc_start: 0.8246 (ptp) cc_final: 0.7232 (pmm) REVERT: A 697 MET cc_start: 0.8342 (ptm) cc_final: 0.8020 (ptm) REVERT: A 746 ASN cc_start: 0.7641 (t0) cc_final: 0.7167 (t0) REVERT: A 756 MET cc_start: 0.7444 (mtm) cc_final: 0.7200 (mtm) REVERT: A 780 ILE cc_start: 0.7957 (mt) cc_final: 0.7688 (mm) REVERT: A 876 MET cc_start: 0.5410 (pmm) cc_final: 0.5189 (pmm) REVERT: A 1118 MET cc_start: 0.7154 (tpp) cc_final: 0.6317 (ttt) REVERT: A 1154 LEU cc_start: 0.7840 (tp) cc_final: 0.7604 (tt) REVERT: A 1200 THR cc_start: 0.8758 (m) cc_final: 0.8505 (p) REVERT: A 1276 GLU cc_start: 0.7538 (tt0) cc_final: 0.7214 (tp30) REVERT: A 1334 GLN cc_start: 0.8259 (mt0) cc_final: 0.7618 (mp10) REVERT: B 150 PHE cc_start: 0.7470 (m-80) cc_final: 0.7011 (m-10) REVERT: B 242 LEU cc_start: 0.8690 (mt) cc_final: 0.8182 (tp) REVERT: B 283 ARG cc_start: 0.9111 (ttt180) cc_final: 0.8821 (ttt-90) REVERT: B 291 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8835 (mm-30) REVERT: B 667 LEU cc_start: 0.9345 (mt) cc_final: 0.9092 (mt) REVERT: B 671 LYS cc_start: 0.9314 (mtpt) cc_final: 0.9028 (mmmt) REVERT: B 692 ILE cc_start: 0.8480 (mm) cc_final: 0.7854 (pt) REVERT: B 697 MET cc_start: 0.8587 (ppp) cc_final: 0.8262 (ppp) REVERT: B 822 ASP cc_start: 0.9354 (m-30) cc_final: 0.8851 (p0) REVERT: B 841 TYR cc_start: 0.6466 (m-80) cc_final: 0.6134 (m-80) REVERT: B 941 ASN cc_start: 0.8944 (m-40) cc_final: 0.8645 (m-40) REVERT: B 1025 PHE cc_start: 0.8098 (m-10) cc_final: 0.7670 (m-10) REVERT: B 1051 MET cc_start: 0.8212 (ttt) cc_final: 0.7966 (mtp) REVERT: B 1178 LYS cc_start: 0.8326 (mttt) cc_final: 0.7521 (pttt) REVERT: B 1210 MET cc_start: 0.8089 (mmt) cc_final: 0.7792 (mmt) REVERT: B 1231 MET cc_start: 0.7558 (tpt) cc_final: 0.7112 (tpt) REVERT: B 1306 PHE cc_start: 0.8161 (m-80) cc_final: 0.7796 (m-80) outliers start: 4 outliers final: 1 residues processed: 254 average time/residue: 0.1774 time to fit residues: 66.0993 Evaluate side-chains 183 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 172 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 212 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 HIS ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.042545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.034308 restraints weight = 216653.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.035497 restraints weight = 148976.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.036417 restraints weight = 109730.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.037138 restraints weight = 84752.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.037697 restraints weight = 68014.681| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21674 Z= 0.138 Angle : 0.594 7.966 29374 Z= 0.307 Chirality : 0.042 0.162 3310 Planarity : 0.004 0.047 3818 Dihedral : 6.163 116.464 2950 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.64 % 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: 0.74 (0.16), residues: 2714 helix: 1.21 (0.13), residues: 1392 sheet: -0.33 (0.27), residues: 344 loop : -0.08 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 238 TYR 0.029 0.001 TYR B1386 PHE 0.016 0.001 PHE B1217 TRP 0.011 0.001 TRP B 416 HIS 0.007 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00284 (21674) covalent geometry : angle 0.59355 (29374) hydrogen bonds : bond 0.03671 ( 1118) hydrogen bonds : angle 4.78970 ( 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 220 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.697 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: A 141 TYR cc_start: 0.8969 (m-80) cc_final: 0.8258 (m-80) REVERT: A 291 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8737 (mm-30) REVERT: A 465 LYS cc_start: 0.9526 (pttm) cc_final: 0.9241 (tptp) REVERT: A 665 LYS cc_start: 0.9741 (pttm) cc_final: 0.9406 (ptpp) REVERT: A 676 MET cc_start: 0.8432 (ptp) cc_final: 0.7433 (pmm) REVERT: A 746 ASN cc_start: 0.7548 (t0) cc_final: 0.7199 (t0) REVERT: A 756 MET cc_start: 0.7623 (mtm) cc_final: 0.7240 (mtm) REVERT: A 1118 MET cc_start: 0.6955 (tpp) cc_final: 0.6004 (ttt) REVERT: A 1200 THR cc_start: 0.8804 (m) cc_final: 0.8583 (p) REVERT: A 1210 MET cc_start: 0.7499 (mmt) cc_final: 0.7157 (mmt) REVERT: B 242 LEU cc_start: 0.8626 (mt) cc_final: 0.8318 (tp) REVERT: B 283 ARG cc_start: 0.9058 (ttt180) cc_final: 0.8776 (ttt-90) REVERT: B 291 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8816 (mm-30) REVERT: B 667 LEU cc_start: 0.9376 (mt) cc_final: 0.9140 (mt) REVERT: B 671 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8875 (mmmt) REVERT: B 692 ILE cc_start: 0.8577 (mm) cc_final: 0.7926 (pt) REVERT: B 697 MET cc_start: 0.8583 (ppp) cc_final: 0.8206 (ppp) REVERT: B 746 ASN cc_start: 0.7197 (t0) cc_final: 0.6677 (t0) REVERT: B 876 MET cc_start: 0.8198 (pmm) cc_final: 0.7921 (pmm) REVERT: B 941 ASN cc_start: 0.8944 (m-40) cc_final: 0.8670 (m-40) REVERT: B 1025 PHE cc_start: 0.8260 (m-10) cc_final: 0.7802 (m-10) REVERT: B 1051 MET cc_start: 0.8086 (ttt) cc_final: 0.7857 (mtp) REVERT: B 1178 LYS cc_start: 0.8209 (mttt) cc_final: 0.7453 (mtmt) REVERT: B 1210 MET cc_start: 0.7931 (mmt) cc_final: 0.7660 (mmt) REVERT: B 1229 MET cc_start: 0.7380 (ptm) cc_final: 0.7172 (ptm) REVERT: B 1231 MET cc_start: 0.7441 (tpt) cc_final: 0.6970 (tpt) REVERT: B 1239 HIS cc_start: 0.8600 (p-80) cc_final: 0.8380 (p-80) REVERT: B 1306 PHE cc_start: 0.8144 (m-80) cc_final: 0.7748 (m-80) REVERT: B 1385 ASN cc_start: 0.8928 (m-40) cc_final: 0.8040 (t0) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1635 time to fit residues: 53.5585 Evaluate side-chains 160 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 72 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 101 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 144 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 GLN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 GLN ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.041639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.033681 restraints weight = 216579.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.034812 restraints weight = 150170.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.035683 restraints weight = 111403.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.036355 restraints weight = 86642.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.036881 restraints weight = 69854.809| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21674 Z= 0.130 Angle : 0.581 8.987 29374 Z= 0.298 Chirality : 0.042 0.256 3310 Planarity : 0.004 0.051 3818 Dihedral : 5.769 112.393 2950 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.47 % 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: 1.09 (0.16), residues: 2714 helix: 1.54 (0.14), residues: 1384 sheet: -0.18 (0.28), residues: 342 loop : 0.03 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 238 TYR 0.022 0.001 TYR B 841 PHE 0.017 0.001 PHE B 522 TRP 0.013 0.001 TRP B 458 HIS 0.015 0.001 HIS B 462 Details of bonding type rmsd covalent geometry : bond 0.00277 (21674) covalent geometry : angle 0.58118 (29374) hydrogen bonds : bond 0.03508 ( 1118) hydrogen bonds : angle 4.64699 ( 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 202 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.782 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: A 141 TYR cc_start: 0.8946 (m-80) cc_final: 0.8199 (m-80) REVERT: A 291 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8756 (mm-30) REVERT: A 326 MET cc_start: 0.6884 (ptp) cc_final: 0.6655 (ptp) REVERT: A 583 MET cc_start: 0.9176 (tmm) cc_final: 0.8903 (mmt) REVERT: A 665 LYS cc_start: 0.9738 (pttm) cc_final: 0.9402 (ptpp) REVERT: A 746 ASN cc_start: 0.7816 (t0) cc_final: 0.7123 (t0) REVERT: A 756 MET cc_start: 0.7770 (mtm) cc_final: 0.7346 (mtm) REVERT: A 1118 MET cc_start: 0.6982 (tpp) cc_final: 0.6185 (ttt) REVERT: A 1334 GLN cc_start: 0.7795 (mt0) cc_final: 0.7559 (mp10) REVERT: B 155 MET cc_start: 0.6040 (mpp) cc_final: 0.5189 (mpp) REVERT: B 283 ARG cc_start: 0.8955 (ttt180) cc_final: 0.8688 (ttt-90) REVERT: B 291 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8808 (mm-30) REVERT: B 541 MET cc_start: 0.7991 (mpp) cc_final: 0.7027 (mpp) REVERT: B 667 LEU cc_start: 0.9420 (mt) cc_final: 0.9054 (mt) REVERT: B 671 LYS cc_start: 0.9278 (mtpt) cc_final: 0.9047 (ptpp) REVERT: B 692 ILE cc_start: 0.8677 (mm) cc_final: 0.8213 (pt) REVERT: B 697 MET cc_start: 0.8687 (ppp) cc_final: 0.8323 (ppp) REVERT: B 746 ASN cc_start: 0.7586 (t0) cc_final: 0.6995 (t0) REVERT: B 876 MET cc_start: 0.8245 (pmm) cc_final: 0.8012 (pmm) REVERT: B 901 MET cc_start: 0.8544 (mmp) cc_final: 0.8342 (tpp) REVERT: B 941 ASN cc_start: 0.8770 (m-40) cc_final: 0.8511 (m-40) REVERT: B 1025 PHE cc_start: 0.8257 (m-10) cc_final: 0.7831 (m-10) REVERT: B 1051 MET cc_start: 0.8153 (ttt) cc_final: 0.7801 (mtp) REVERT: B 1210 MET cc_start: 0.7952 (mmt) cc_final: 0.7725 (mmt) REVERT: B 1231 MET cc_start: 0.7643 (tpt) cc_final: 0.7185 (tpt) REVERT: B 1239 HIS cc_start: 0.8583 (p-80) cc_final: 0.8324 (p-80) REVERT: B 1306 PHE cc_start: 0.8053 (m-80) cc_final: 0.7786 (m-80) REVERT: B 1385 ASN cc_start: 0.9044 (m-40) cc_final: 0.8173 (t0) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1527 time to fit residues: 46.5513 Evaluate side-chains 151 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 228 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 GLN ** B1309 HIS ** 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 = 0.3403 r_free = 0.3403 target = 0.037680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.030240 restraints weight = 230518.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.031319 restraints weight = 155236.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.032139 restraints weight = 113179.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.032761 restraints weight = 86987.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.033248 restraints weight = 69767.112| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 21674 Z= 0.217 Angle : 0.688 7.557 29374 Z= 0.357 Chirality : 0.044 0.204 3310 Planarity : 0.005 0.050 3818 Dihedral : 5.850 112.423 2950 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.79 (0.16), residues: 2714 helix: 1.29 (0.14), residues: 1368 sheet: -0.37 (0.28), residues: 350 loop : -0.07 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1278 TYR 0.019 0.002 TYR A 625 PHE 0.022 0.002 PHE A 626 TRP 0.017 0.002 TRP A 135 HIS 0.009 0.002 HIS A1239 Details of bonding type rmsd covalent geometry : bond 0.00446 (21674) covalent geometry : angle 0.68839 (29374) hydrogen bonds : bond 0.04036 ( 1118) hydrogen bonds : angle 5.06664 ( 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 175 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.789 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: A 141 TYR cc_start: 0.9049 (m-80) cc_final: 0.8314 (m-10) REVERT: A 291 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 756 MET cc_start: 0.7927 (mtm) cc_final: 0.7342 (mtm) REVERT: A 892 LEU cc_start: 0.9106 (mt) cc_final: 0.8689 (mt) REVERT: A 899 MET cc_start: 0.6656 (mtp) cc_final: 0.4805 (mtp) REVERT: A 901 MET cc_start: 0.8785 (mmm) cc_final: 0.7899 (mmm) REVERT: A 1118 MET cc_start: 0.7585 (tpp) cc_final: 0.6632 (ttt) REVERT: A 1210 MET cc_start: 0.7550 (mmt) cc_final: 0.7266 (mmm) REVERT: B 155 MET cc_start: 0.6295 (mpp) cc_final: 0.5905 (mpp) REVERT: B 283 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8637 (ttt90) REVERT: B 291 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8898 (mm-30) REVERT: B 697 MET cc_start: 0.8824 (ppp) cc_final: 0.8510 (ppp) REVERT: B 746 ASN cc_start: 0.8128 (t0) cc_final: 0.7569 (t0) REVERT: B 1210 MET cc_start: 0.7786 (mmt) cc_final: 0.7570 (mmt) REVERT: B 1231 MET cc_start: 0.7879 (tpt) cc_final: 0.7515 (tpt) REVERT: B 1239 HIS cc_start: 0.8961 (p-80) cc_final: 0.8651 (p90) REVERT: B 1275 MET cc_start: 0.8452 (mmp) cc_final: 0.8126 (mmm) REVERT: B 1385 ASN cc_start: 0.9184 (m-40) cc_final: 0.8263 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1429 time to fit residues: 38.2472 Evaluate side-chains 137 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 191 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 206 optimal weight: 0.1980 chunk 265 optimal weight: 0.1980 chunk 221 optimal weight: 0.2980 chunk 162 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 ASN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 GLN ** B1309 HIS ** 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 = 0.3479 r_free = 0.3479 target = 0.040142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.032192 restraints weight = 219304.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.033349 restraints weight = 148454.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.034240 restraints weight = 108027.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.034919 restraints weight = 82922.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.035450 restraints weight = 66180.947| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21674 Z= 0.108 Angle : 0.575 8.036 29374 Z= 0.292 Chirality : 0.042 0.187 3310 Planarity : 0.004 0.054 3818 Dihedral : 5.339 116.349 2950 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 1.18 (0.17), residues: 2714 helix: 1.62 (0.14), residues: 1374 sheet: 0.17 (0.30), residues: 332 loop : -0.06 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 238 TYR 0.013 0.001 TYR B1386 PHE 0.017 0.001 PHE B 454 TRP 0.029 0.002 TRP B 135 HIS 0.006 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00228 (21674) covalent geometry : angle 0.57518 (29374) hydrogen bonds : bond 0.03251 ( 1118) hydrogen bonds : angle 4.61235 ( 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 189 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9484 (mt) cc_final: 0.9221 (mt) REVERT: A 141 TYR cc_start: 0.8991 (m-80) cc_final: 0.8596 (m-80) REVERT: A 291 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8770 (mm-30) REVERT: A 665 LYS cc_start: 0.9772 (pttm) cc_final: 0.9504 (ptpt) REVERT: A 746 ASN cc_start: 0.8646 (t0) cc_final: 0.8079 (t0) REVERT: A 756 MET cc_start: 0.7804 (mtm) cc_final: 0.7394 (mtm) REVERT: A 892 LEU cc_start: 0.9070 (mt) cc_final: 0.8774 (mt) REVERT: A 899 MET cc_start: 0.6562 (mtp) cc_final: 0.4767 (mtp) REVERT: A 901 MET cc_start: 0.8675 (mmm) cc_final: 0.7813 (mmm) REVERT: A 1118 MET cc_start: 0.7288 (tpp) cc_final: 0.6173 (ttm) REVERT: B 283 ARG cc_start: 0.8945 (ttt180) cc_final: 0.8727 (ttt90) REVERT: B 291 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8871 (mm-30) REVERT: B 746 ASN cc_start: 0.8068 (t0) cc_final: 0.7646 (t0) REVERT: B 1025 PHE cc_start: 0.8466 (m-80) cc_final: 0.7759 (m-10) REVERT: B 1275 MET cc_start: 0.8385 (mmp) cc_final: 0.7960 (mmm) REVERT: B 1385 ASN cc_start: 0.8981 (m-40) cc_final: 0.8172 (t0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1446 time to fit residues: 42.2899 Evaluate side-chains 146 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 263 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 247 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1309 HIS ** 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 = 0.3458 r_free = 0.3458 target = 0.039378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.031571 restraints weight = 214296.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.032712 restraints weight = 143909.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.033590 restraints weight = 104100.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.034271 restraints weight = 79319.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.034786 restraints weight = 62945.359| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21674 Z= 0.118 Angle : 0.575 12.450 29374 Z= 0.292 Chirality : 0.042 0.181 3310 Planarity : 0.004 0.056 3818 Dihedral : 5.199 115.614 2950 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 1.24 (0.17), residues: 2714 helix: 1.68 (0.14), residues: 1380 sheet: 0.18 (0.30), residues: 336 loop : -0.05 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 423 TYR 0.016 0.001 TYR B1386 PHE 0.018 0.001 PHE B 454 TRP 0.014 0.001 TRP B 135 HIS 0.005 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00251 (21674) covalent geometry : angle 0.57493 (29374) hydrogen bonds : bond 0.03263 ( 1118) hydrogen bonds : angle 4.56624 ( 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 174 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.809 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: A 141 TYR cc_start: 0.9000 (m-80) cc_final: 0.8625 (m-80) REVERT: A 291 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8818 (mm-30) REVERT: A 326 MET cc_start: 0.7114 (ptp) cc_final: 0.6547 (mpp) REVERT: A 667 LEU cc_start: 0.9566 (mm) cc_final: 0.9319 (mm) REVERT: A 746 ASN cc_start: 0.8387 (t0) cc_final: 0.7798 (t0) REVERT: A 756 MET cc_start: 0.7858 (mtm) cc_final: 0.7339 (mtm) REVERT: A 892 LEU cc_start: 0.9134 (mt) cc_final: 0.8827 (mt) REVERT: A 899 MET cc_start: 0.6605 (mtp) cc_final: 0.4881 (mtp) REVERT: A 901 MET cc_start: 0.8719 (mmm) cc_final: 0.7954 (mmm) REVERT: A 1118 MET cc_start: 0.7296 (tpp) cc_final: 0.6136 (ttt) REVERT: B 283 ARG cc_start: 0.8933 (ttt180) cc_final: 0.8712 (ttt90) REVERT: B 291 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8879 (mm-30) REVERT: B 746 ASN cc_start: 0.8099 (t0) cc_final: 0.7682 (t0) REVERT: B 1210 MET cc_start: 0.7578 (mmt) cc_final: 0.7339 (mmt) REVERT: B 1275 MET cc_start: 0.8312 (mmp) cc_final: 0.7964 (mmm) REVERT: B 1385 ASN cc_start: 0.8952 (m-40) cc_final: 0.8114 (t0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1441 time to fit residues: 38.9987 Evaluate side-chains 132 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 210 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 ASN A1297 ASN ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.037875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.030342 restraints weight = 228818.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.031416 restraints weight = 153053.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.032237 restraints weight = 111076.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.032867 restraints weight = 85066.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.033350 restraints weight = 68028.390| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21674 Z= 0.161 Angle : 0.624 12.132 29374 Z= 0.319 Chirality : 0.043 0.197 3310 Planarity : 0.004 0.056 3818 Dihedral : 5.324 111.595 2950 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1.01 (0.17), residues: 2714 helix: 1.57 (0.14), residues: 1368 sheet: -0.21 (0.29), residues: 356 loop : -0.14 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 238 TYR 0.023 0.002 TYR B1094 PHE 0.018 0.002 PHE B1217 TRP 0.010 0.001 TRP A 399 HIS 0.006 0.001 HIS B1020 Details of bonding type rmsd covalent geometry : bond 0.00339 (21674) covalent geometry : angle 0.62429 (29374) hydrogen bonds : bond 0.03502 ( 1118) hydrogen bonds : angle 4.80660 ( 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 164 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.740 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: A 141 TYR cc_start: 0.9057 (m-80) cc_final: 0.8678 (m-80) REVERT: A 291 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8796 (mm-30) REVERT: A 697 MET cc_start: 0.8287 (pmm) cc_final: 0.7960 (pmm) REVERT: A 746 ASN cc_start: 0.8411 (t0) cc_final: 0.7708 (t0) REVERT: A 756 MET cc_start: 0.7947 (mtm) cc_final: 0.7458 (mtm) REVERT: A 817 MET cc_start: 0.7214 (ttm) cc_final: 0.6956 (ttm) REVERT: A 892 LEU cc_start: 0.9331 (mt) cc_final: 0.8921 (mt) REVERT: A 899 MET cc_start: 0.6892 (mtp) cc_final: 0.5080 (mtp) REVERT: A 901 MET cc_start: 0.8946 (mmm) cc_final: 0.8190 (mmm) REVERT: B 291 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8879 (mm-30) REVERT: B 597 GLN cc_start: 0.9578 (mp10) cc_final: 0.9276 (pm20) REVERT: B 785 MET cc_start: 0.7316 (mmp) cc_final: 0.6889 (tpp) REVERT: B 876 MET cc_start: 0.8459 (pmm) cc_final: 0.8169 (pmm) REVERT: B 1231 MET cc_start: 0.7779 (tpt) cc_final: 0.7498 (tpt) REVERT: B 1275 MET cc_start: 0.8387 (mmp) cc_final: 0.8017 (mmm) REVERT: B 1385 ASN cc_start: 0.9016 (m-40) cc_final: 0.8195 (t0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1694 time to fit residues: 42.8492 Evaluate side-chains 129 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 0.0000 chunk 195 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 270 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN B 664 GLN ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1309 HIS ** 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 = 0.3474 r_free = 0.3474 target = 0.040010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.032026 restraints weight = 209385.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.033184 restraints weight = 140489.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.034048 restraints weight = 101768.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.034730 restraints weight = 77859.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.035259 restraints weight = 61991.984| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21674 Z= 0.107 Angle : 0.580 9.686 29374 Z= 0.294 Chirality : 0.043 0.184 3310 Planarity : 0.004 0.058 3818 Dihedral : 5.070 113.329 2950 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.20 (0.17), residues: 2714 helix: 1.67 (0.14), residues: 1372 sheet: 0.18 (0.30), residues: 336 loop : -0.10 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.014 0.001 TYR B1386 PHE 0.019 0.001 PHE B 454 TRP 0.012 0.001 TRP B 135 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00221 (21674) covalent geometry : angle 0.57963 (29374) hydrogen bonds : bond 0.03140 ( 1118) hydrogen bonds : angle 4.51291 ( 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 178 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.890 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: A 141 TYR cc_start: 0.8987 (m-80) cc_final: 0.8558 (m-80) REVERT: A 291 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8795 (mm-30) REVERT: A 549 ASN cc_start: 0.9489 (t0) cc_final: 0.9165 (p0) REVERT: A 676 MET cc_start: 0.8243 (ptm) cc_final: 0.7796 (pmm) REVERT: A 697 MET cc_start: 0.7972 (pmm) cc_final: 0.7682 (pmm) REVERT: A 746 ASN cc_start: 0.8361 (t0) cc_final: 0.7649 (t0) REVERT: A 756 MET cc_start: 0.7838 (mtm) cc_final: 0.7401 (mtm) REVERT: A 817 MET cc_start: 0.7177 (ttm) cc_final: 0.6869 (ttm) REVERT: A 822 ASP cc_start: 0.9349 (m-30) cc_final: 0.8931 (m-30) REVERT: A 892 LEU cc_start: 0.9285 (mt) cc_final: 0.8974 (mt) REVERT: A 899 MET cc_start: 0.6676 (mtp) cc_final: 0.4976 (mtp) REVERT: A 901 MET cc_start: 0.8748 (mmm) cc_final: 0.8068 (mmm) REVERT: B 291 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8858 (mm-30) REVERT: B 542 MET cc_start: 0.9309 (mtm) cc_final: 0.9003 (mtt) REVERT: B 746 ASN cc_start: 0.8094 (t0) cc_final: 0.7774 (t0) REVERT: B 785 MET cc_start: 0.7116 (mmp) cc_final: 0.6676 (tpp) REVERT: B 876 MET cc_start: 0.8360 (pmm) cc_final: 0.8125 (pmm) REVERT: B 1051 MET cc_start: 0.7718 (mtp) cc_final: 0.7004 (mtm) REVERT: B 1178 LYS cc_start: 0.7661 (mmpt) cc_final: 0.6558 (mtmt) REVERT: B 1275 MET cc_start: 0.8132 (mmp) cc_final: 0.7904 (mmm) REVERT: B 1385 ASN cc_start: 0.8841 (m-40) cc_final: 0.8044 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1560 time to fit residues: 43.3536 Evaluate side-chains 135 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 168 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 chunk 165 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.037751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.030191 restraints weight = 220728.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031279 restraints weight = 147194.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.032106 restraints weight = 106247.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.032739 restraints weight = 81063.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.033235 restraints weight = 64654.405| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.7618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21674 Z= 0.162 Angle : 0.621 10.156 29374 Z= 0.318 Chirality : 0.043 0.199 3310 Planarity : 0.005 0.056 3818 Dihedral : 5.205 109.805 2950 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 1.08 (0.17), residues: 2714 helix: 1.62 (0.14), residues: 1368 sheet: -0.13 (0.29), residues: 356 loop : -0.13 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 238 TYR 0.019 0.002 TYR B1386 PHE 0.017 0.002 PHE B 454 TRP 0.010 0.002 TRP A 651 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00342 (21674) covalent geometry : angle 0.62140 (29374) hydrogen bonds : bond 0.03482 ( 1118) hydrogen bonds : angle 4.78711 ( 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 163 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.898 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: A 141 TYR cc_start: 0.9064 (m-80) cc_final: 0.8658 (m-80) REVERT: A 291 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8790 (mm-30) REVERT: A 549 ASN cc_start: 0.9504 (t0) cc_final: 0.9216 (p0) REVERT: A 676 MET cc_start: 0.8373 (ptm) cc_final: 0.7835 (pmm) REVERT: A 697 MET cc_start: 0.8269 (pmm) cc_final: 0.7976 (pmm) REVERT: A 746 ASN cc_start: 0.8503 (t0) cc_final: 0.7792 (t0) REVERT: A 756 MET cc_start: 0.7983 (mtm) cc_final: 0.7551 (mtm) REVERT: A 892 LEU cc_start: 0.9251 (mt) cc_final: 0.8956 (mt) REVERT: A 899 MET cc_start: 0.7021 (mtp) cc_final: 0.5399 (mtp) REVERT: A 901 MET cc_start: 0.8896 (mmm) cc_final: 0.8162 (mmm) REVERT: B 291 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8898 (mm-30) REVERT: B 542 MET cc_start: 0.9278 (mtm) cc_final: 0.8948 (mtt) REVERT: B 785 MET cc_start: 0.7570 (mmp) cc_final: 0.6896 (tpp) REVERT: B 876 MET cc_start: 0.8608 (pmm) cc_final: 0.8272 (pmm) REVERT: B 1051 MET cc_start: 0.8042 (mtp) cc_final: 0.7259 (mtm) REVERT: B 1178 LYS cc_start: 0.7949 (mmpt) cc_final: 0.6470 (mtmt) REVERT: B 1231 MET cc_start: 0.7759 (tpt) cc_final: 0.7526 (tpp) REVERT: B 1275 MET cc_start: 0.8415 (mmp) cc_final: 0.7989 (mmm) REVERT: B 1385 ASN cc_start: 0.8923 (m-40) cc_final: 0.8086 (t0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1610 time to fit residues: 41.1049 Evaluate side-chains 130 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 265 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN ** A1309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 960 HIS ** 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 = 0.3387 r_free = 0.3387 target = 0.037384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.029857 restraints weight = 227137.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.030938 restraints weight = 150636.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031743 restraints weight = 108816.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.032364 restraints weight = 83224.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.032847 restraints weight = 66617.984| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21674 Z= 0.157 Angle : 0.616 8.716 29374 Z= 0.315 Chirality : 0.043 0.206 3310 Planarity : 0.004 0.058 3818 Dihedral : 5.187 103.066 2950 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.06 (0.17), residues: 2714 helix: 1.58 (0.14), residues: 1362 sheet: -0.19 (0.29), residues: 358 loop : -0.07 (0.22), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 313 TYR 0.017 0.002 TYR B1386 PHE 0.016 0.002 PHE B 454 TRP 0.009 0.001 TRP A 651 HIS 0.007 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00332 (21674) covalent geometry : angle 0.61642 (29374) hydrogen bonds : bond 0.03445 ( 1118) hydrogen bonds : angle 4.84892 ( 3246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.95 seconds wall clock time: 54 minutes 38.17 seconds (3278.17 seconds total)