Starting phenix.real_space_refine on Mon Jul 6 09:20:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m8e_23716/07_2026/7m8e_23716.cif" } resolution = 3.4 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= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 135 5.16 5 C 21059 2.51 5 N 6009 2.21 5 O 6625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 10396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10396 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7719 Classifications: {'peptide': 967} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 931} Chain: "1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "2" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "3" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14581 SG CYS D 70 67.582 123.454 124.282 1.00132.86 S ATOM 14595 SG CYS D 72 70.497 125.753 124.707 1.00136.55 S ATOM 14703 SG CYS D 85 67.111 127.434 123.997 1.00139.51 S ATOM 14727 SG CYS D 88 69.263 125.813 121.546 1.00137.43 S ATOM 20415 SG CYS D 814 28.023 95.049 73.037 1.00100.48 S ATOM 20980 SG CYS D 888 31.566 96.196 74.097 1.00 96.21 S ATOM 21031 SG CYS D 895 29.747 93.284 75.690 1.00 86.90 S ATOM 21052 SG CYS D 898 31.006 92.760 72.479 1.00 87.17 S Time building chain proxies: 6.68, per 1000 atoms: 0.20 Number of scatterers: 33880 At special positions: 0 Unit cell: (163.76, 165.54, 211.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 135 16.00 P 49 15.00 Mg 1 11.99 O 6625 8.00 N 6009 7.00 C 21059 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 12 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7760 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 54 sheets defined 39.1% alpha, 13.8% beta 7 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 4.215A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.653A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.038A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.054A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 4.326A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.043A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.193A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.511A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.601A pdb=" N ILE C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.616A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.546A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.436A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.770A pdb=" N MET C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.754A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.868A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.539A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.574A pdb=" N ASP C 674 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 Processing helix chain 'C' and resid 686 through 689 removed outlier: 4.234A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 689' Processing helix chain 'C' and resid 705 through 712 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.515A pdb=" N ALA C 861 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.180A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 4.348A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1038 removed outlier: 3.631A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.645A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.912A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 4.035A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.534A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1265 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.590A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C1282 " --> pdb=" O LEU C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.980A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.645A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.695A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.597A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 4.422A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.639A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.722A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.370A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 3.751A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.763A pdb=" N ILE D 381 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.796A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.866A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 3.684A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.676A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.539A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.930A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.568A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.593A pdb=" N ILE D 654 " --> pdb=" O LYS D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 702 removed outlier: 3.571A pdb=" N TYR D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 769 through 787 removed outlier: 4.496A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 804 Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 removed outlier: 4.130A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.750A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.653A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.501A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1288 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.919A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 4.145A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1362 removed outlier: 3.770A pdb=" N GLY D1362 " --> pdb=" O ALA D1359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1359 through 1362' Processing helix chain 'D' and resid 1363 through 1373 removed outlier: 3.662A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.931A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.845A pdb=" N LEU E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 17 Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 110 through 118 removed outlier: 3.947A pdb=" N ARG F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 141 removed outlier: 4.349A pdb=" N PHE F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 167 removed outlier: 4.405A pdb=" N ILE F 161 " --> pdb=" O HIS F 157 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 167 " --> pdb=" O HIS F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.542A pdb=" N SER F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 223 Processing helix chain 'F' and resid 231 through 242 removed outlier: 4.173A pdb=" N HIS F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 255 through 260 Processing helix chain 'F' and resid 262 through 271 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.967A pdb=" N ALA F 298 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 319 removed outlier: 3.988A pdb=" N GLN F 318 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.598A pdb=" N SER F 323 " --> pdb=" O GLY F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.664A pdb=" N ARG F 329 " --> pdb=" O PHE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 361 removed outlier: 4.196A pdb=" N PHE F 342 " --> pdb=" O ASP F 338 " (cutoff:3.500A) Proline residue: F 351 - end of helix Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.849A pdb=" N ASN F 371 " --> pdb=" O ASN F 367 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 391 removed outlier: 4.106A pdb=" N LEU F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 388 " --> pdb=" O PRO F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 Processing helix chain 'F' and resid 441 through 452 removed outlier: 4.003A pdb=" N GLN F 445 " --> pdb=" O PRO F 441 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL F 450 " --> pdb=" O THR F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'F' and resid 470 through 479 removed outlier: 3.987A pdb=" N GLU F 476 " --> pdb=" O ARG F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 487 removed outlier: 3.715A pdb=" N ASN F 486 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE F 487 " --> pdb=" O TRP F 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 483 through 487' Processing helix chain 'F' and resid 488 through 500 removed outlier: 4.165A pdb=" N GLU F 492 " --> pdb=" O ASP F 488 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 500 " --> pdb=" O GLY F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 528 Processing helix chain 'F' and resid 540 through 551 removed outlier: 3.636A pdb=" N ASP F 544 " --> pdb=" O ILE F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 596 removed outlier: 3.694A pdb=" N LEU F 590 " --> pdb=" O ASN F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 629 removed outlier: 3.794A pdb=" N ARG F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.922A pdb=" N ILE F 642 " --> pdb=" O THR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 656 Processing helix chain 'F' and resid 662 through 683 removed outlier: 3.790A pdb=" N LEU F 666 " --> pdb=" O GLY F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 694 removed outlier: 3.798A pdb=" N GLU F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 710 removed outlier: 3.546A pdb=" N GLN F 700 " --> pdb=" O GLY F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 727 removed outlier: 3.846A pdb=" N ASN F 721 " --> pdb=" O ALA F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 771 removed outlier: 3.643A pdb=" N ALA F 768 " --> pdb=" O ASP F 764 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 794 removed outlier: 3.838A pdb=" N GLY F 794 " --> pdb=" O LEU F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 835 removed outlier: 6.691A pdb=" N LEU F 832 " --> pdb=" O GLN F 829 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN F 833 " --> pdb=" O LEU F 830 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 834 " --> pdb=" O GLN F 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 857 through 863 Processing helix chain 'F' and resid 869 through 877 removed outlier: 3.505A pdb=" N VAL F 877 " --> pdb=" O GLY F 873 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 926 removed outlier: 3.630A pdb=" N VAL F 884 " --> pdb=" O VAL F 880 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS F 885 " --> pdb=" O GLN F 881 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN F 889 " --> pdb=" O HIS F 885 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU F 890 " --> pdb=" O ALA F 886 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY F 891 " --> pdb=" O ILE F 887 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F 893 " --> pdb=" O GLN F 889 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN F 894 " --> pdb=" O LEU F 890 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU F 896 " --> pdb=" O GLU F 892 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS F 897 " --> pdb=" O ALA F 893 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU F 914 " --> pdb=" O ALA F 910 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER F 915 " --> pdb=" O ASP F 911 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 923 " --> pdb=" O SER F 919 " (cutoff:3.500A) Processing helix chain 'F' and resid 932 through 951 removed outlier: 4.024A pdb=" N LEU F 936 " --> pdb=" O ARG F 932 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.451A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 25 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.821A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.705A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.609A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.613A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.613A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.059A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.892A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.564A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N ALA C 94 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N MET C 124 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 96 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 122 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 98 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 100 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY C 112 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.587A pdb=" N ILE C 138 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 141 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.570A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.036A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'C' and resid 598 through 606 removed outlier: 5.288A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 634 through 638 Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.572A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 5.946A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 759 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 798 through 802 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.562A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.809A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1209 through 1210 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.796A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1338 through 1339 Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 149 removed outlier: 6.842A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.228A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 548 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.148A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 949 through 951 Processing sheet with id=AE5, first strand: chain 'D' and resid 991 through 995 removed outlier: 3.682A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.925A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AE9, first strand: chain 'D' and resid 1106 through 1107 removed outlier: 4.135A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AF2, first strand: chain 'D' and resid 1263 through 1265 Processing sheet with id=AF3, first strand: chain 'F' and resid 39 through 44 removed outlier: 6.838A pdb=" N THR F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL F 25 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR F 31 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.576A pdb=" N ILE F 61 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL F 71 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR F 86 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 228 through 229 removed outlier: 7.009A pdb=" N ALA F 228 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL F 203 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N CYS F 254 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE F 205 " --> pdb=" O CYS F 254 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU F 277 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU F 312 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL F 279 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 173 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 311 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE F 418 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU F 174 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 431 through 433 removed outlier: 6.597A pdb=" N GLU F 432 " --> pdb=" O ILE F 608 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F 507 " --> pdb=" O VAL F 579 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 436 through 438 removed outlier: 6.468A pdb=" N ILE F 436 " --> pdb=" O TYR F 612 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 728 through 732 removed outlier: 7.243A pdb=" N THR F 760 " --> pdb=" O GLN F 775 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 799 through 805 removed outlier: 7.185A pdb=" N THR F 800 " --> pdb=" O LEU F 962 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N VAL F 964 " --> pdb=" O THR F 800 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER F 802 " --> pdb=" O VAL F 964 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR F 966 " --> pdb=" O SER F 802 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 804 " --> pdb=" O THR F 966 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE F 819 " --> pdb=" O ASP F 958 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU F 960 " --> pdb=" O GLU F 817 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU F 817 " --> pdb=" O LEU F 960 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU F 962 " --> pdb=" O LEU F 815 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU F 815 " --> pdb=" O LEU F 962 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 8.25 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8852 1.33 - 1.45: 5980 1.45 - 1.57: 19350 1.57 - 1.69: 94 1.69 - 1.81: 236 Bond restraints: 34512 Sorted by residual: bond pdb=" C4' DT 2 13 " pdb=" C3' DT 2 13 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.00e-02 1.00e+04 1.00e+01 bond pdb=" C3' DC 1 78 " pdb=" C2' DC 1 78 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C3' DG 2 22 " pdb=" C2' DG 2 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" C4' DA 2 15 " pdb=" C3' DA 2 15 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.00e-02 1.00e+04 9.70e+00 bond pdb=" C3' DT 2 13 " pdb=" O3' DT 2 13 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 8.88e+00 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 45528 2.50 - 5.01: 1174 5.01 - 7.51: 130 7.51 - 10.02: 18 10.02 - 12.52: 6 Bond angle restraints: 46856 Sorted by residual: angle pdb=" N ARG D 77 " pdb=" CA ARG D 77 " pdb=" C ARG D 77 " ideal model delta sigma weight residual 110.80 123.32 -12.52 2.13e+00 2.20e-01 3.46e+01 angle pdb=" C ARG D 362 " pdb=" N LEU D 363 " pdb=" CA LEU D 363 " ideal model delta sigma weight residual 121.54 112.35 9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C PHE C 804 " pdb=" N MET C 805 " pdb=" CA MET C 805 " ideal model delta sigma weight residual 122.56 130.14 -7.58 1.58e+00 4.01e-01 2.30e+01 angle pdb=" C ILE B 16 " pdb=" N GLU B 17 " pdb=" CA GLU B 17 " ideal model delta sigma weight residual 123.11 116.46 6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" O4' DT 2 21 " pdb=" C4' DT 2 21 " pdb=" C3' DT 2 21 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 46851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 20519 33.02 - 66.03: 489 66.03 - 99.05: 44 99.05 - 132.07: 1 132.07 - 165.09: 1 Dihedral angle restraints: 21054 sinusoidal: 9017 harmonic: 12037 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 -123.94 -56.06 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA GLU C 908 " pdb=" C GLU C 908 " pdb=" N LYS C 909 " pdb=" CA LYS C 909 " ideal model delta harmonic sigma weight residual 180.00 129.77 50.23 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA LYS D 76 " pdb=" C LYS D 76 " pdb=" N ARG D 77 " pdb=" CA ARG D 77 " ideal model delta harmonic sigma weight residual 180.00 140.23 39.77 0 5.00e+00 4.00e-02 6.33e+01 ... (remaining 21051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4284 0.070 - 0.140: 946 0.140 - 0.209: 80 0.209 - 0.279: 6 0.279 - 0.349: 1 Chirality restraints: 5317 Sorted by residual: chirality pdb=" CA PHE C 804 " pdb=" N PHE C 804 " pdb=" C PHE C 804 " pdb=" CB PHE C 804 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL C 714 " pdb=" CA VAL C 714 " pdb=" CG1 VAL C 714 " pdb=" CG2 VAL C 714 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR C 356 " pdb=" CA THR C 356 " pdb=" OG1 THR C 356 " pdb=" CG2 THR C 356 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 5314 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 520 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 908 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" CD GLU C 908 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU C 908 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU C 908 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 358 " -0.051 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO D 359 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 359 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 359 " -0.042 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 222 2.52 - 3.11: 26105 3.11 - 3.71: 47336 3.71 - 4.30: 64668 4.30 - 4.90: 109771 Nonbonded interactions: 248102 Sorted by model distance: nonbonded pdb=" O3' A 3 9 " pdb="MG MG D1503 " model vdw 1.923 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 1.963 2.170 nonbonded pdb=" O SER D 961 " pdb=" OG1 THR D 980 " model vdw 2.056 3.040 nonbonded pdb=" OD1 ASP C 81 " pdb=" N VAL C 82 " model vdw 2.061 3.120 nonbonded pdb=" OG1 THR C 216 " pdb=" OE1 GLU C 218 " model vdw 2.105 3.040 ... (remaining 248097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) 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 individual isotropic 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: 3.780 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.840 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 : 0.010 0.083 34520 Z= 0.424 Angle : 0.974 14.877 46868 Z= 0.542 Chirality : 0.056 0.349 5317 Planarity : 0.006 0.104 5999 Dihedral : 14.631 165.085 13294 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.64 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.81 % Twisted General : 0.20 % 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: -2.61 (0.12), residues: 4165 helix: -0.66 (0.13), residues: 1467 sheet: -1.48 (0.21), residues: 542 loop : -2.64 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 312 TYR 0.028 0.003 TYR D 140 PHE 0.050 0.003 PHE C 804 TRP 0.039 0.002 TRP F 624 HIS 0.020 0.002 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.01002 / 0.42 (34512) covalent geometry : angle 0.96710 / 0.54 (46856) hydrogen bonds : bond 0.17618 / 12.27 ( 1278) hydrogen bonds : angle 7.17995 / 4.96 ( 3586) metal coordination : bond 0.02826 / 1.75 ( 8) metal coordination : angle 7.17480 / 4.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9093 (mppt) cc_final: 0.8415 (mptt) REVERT: C 949 GLU cc_start: 0.8352 (pp20) cc_final: 0.8018 (pp20) REVERT: C 950 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8245 (tm-30) REVERT: C 952 GLN cc_start: 0.8050 (tt0) cc_final: 0.7587 (tm-30) REVERT: C 1033 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7740 (ttp80) REVERT: D 66 LYS cc_start: 0.8136 (tttm) cc_final: 0.7899 (tttm) REVERT: D 151 MET cc_start: 0.1958 (ttp) cc_final: 0.1370 (tmm) REVERT: D 177 ASP cc_start: 0.7360 (m-30) cc_final: 0.7152 (m-30) REVERT: D 725 MET cc_start: 0.8887 (mtm) cc_final: 0.8608 (mtm) REVERT: D 1040 MET cc_start: -0.0301 (pmm) cc_final: -0.0576 (mtt) REVERT: D 1152 GLU cc_start: 0.7247 (mp0) cc_final: 0.6959 (mp0) REVERT: D 1208 ASP cc_start: 0.8047 (t0) cc_final: 0.7177 (m-30) REVERT: D 1327 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7388 (mm-30) REVERT: D 1370 MET cc_start: 0.8605 (ttp) cc_final: 0.8389 (ttm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2169 time to fit residues: 107.5200 Evaluate side-chains 249 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132343 restraints weight = 47598.143| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.00 r_work: 0.3343 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34520 Z= 0.189 Angle : 0.734 11.906 46868 Z= 0.385 Chirality : 0.047 0.305 5317 Planarity : 0.005 0.094 5999 Dihedral : 11.026 164.925 5104 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 0.65 % Allowed : 7.55 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.20 % 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: -2.07 (0.12), residues: 4165 helix: -0.14 (0.13), residues: 1501 sheet: -1.27 (0.22), residues: 541 loop : -2.38 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 312 TYR 0.019 0.002 TYR C 105 PHE 0.031 0.002 PHE C 804 TRP 0.012 0.001 TRP F 624 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (34512) covalent geometry : angle 0.73044 / 0.39 (46856) hydrogen bonds : bond 0.06360 / 4.38 ( 1278) hydrogen bonds : angle 5.38942 / 3.77 ( 3586) metal coordination : bond 0.01096 / 0.66 ( 8) metal coordination : angle 4.38940 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9052 (mppt) cc_final: 0.8606 (mptt) REVERT: C 472 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7751 (tm-30) REVERT: C 800 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: C 952 GLN cc_start: 0.8100 (tt0) cc_final: 0.7714 (tm-30) REVERT: C 1029 LEU cc_start: 0.8458 (tp) cc_final: 0.8213 (tt) REVERT: C 1033 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8000 (ttp80) REVERT: D 66 LYS cc_start: 0.8541 (tttm) cc_final: 0.8329 (tttm) REVERT: D 1174 ARG cc_start: 0.7495 (mpt180) cc_final: 0.7064 (mpt180) REVERT: D 1208 ASP cc_start: 0.8005 (t0) cc_final: 0.7218 (m-30) REVERT: D 1370 MET cc_start: 0.8793 (ttp) cc_final: 0.8524 (ttm) outliers start: 23 outliers final: 13 residues processed: 309 average time/residue: 0.2129 time to fit residues: 108.3307 Evaluate side-chains 267 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 884 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 253 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 397 optimal weight: 20.0000 chunk 379 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 387 ASN C1013 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134511 restraints weight = 47474.051| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.86 r_work: 0.3395 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34520 Z= 0.133 Angle : 0.621 11.115 46868 Z= 0.327 Chirality : 0.044 0.275 5317 Planarity : 0.004 0.074 5999 Dihedral : 10.775 163.858 5104 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 1.26 % Allowed : 10.75 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.12 % 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: -1.59 (0.13), residues: 4165 helix: 0.35 (0.14), residues: 1498 sheet: -0.98 (0.22), residues: 538 loop : -2.18 (0.12), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 28 TYR 0.018 0.001 TYR C 367 PHE 0.026 0.001 PHE D1274 TRP 0.008 0.001 TRP D 868 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (34512) covalent geometry : angle 0.61816 / 0.33 (46856) hydrogen bonds : bond 0.04991 / 3.44 ( 1278) hydrogen bonds : angle 4.86649 / 3.40 ( 3586) metal coordination : bond 0.00680 / 0.40 ( 8) metal coordination : angle 3.77507 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 GLU cc_start: 0.7734 (tp30) cc_final: 0.7120 (tt0) REVERT: C 151 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7108 (ttt180) REVERT: C 472 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 504 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 800 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: C 952 GLN cc_start: 0.8102 (tt0) cc_final: 0.7637 (tm-30) REVERT: C 1013 GLN cc_start: 0.5066 (OUTLIER) cc_final: 0.4603 (mm-40) REVERT: C 1014 LEU cc_start: 0.5680 (mm) cc_final: 0.5356 (mm) REVERT: C 1033 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7929 (ttp80) REVERT: C 1304 MET cc_start: 0.8992 (tpp) cc_final: 0.8656 (tpp) REVERT: C 1306 LYS cc_start: 0.8969 (tppp) cc_final: 0.8686 (tttm) REVERT: D 821 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7921 (mtm) REVERT: D 1174 ARG cc_start: 0.7438 (mpt180) cc_final: 0.6641 (mmt-90) REVERT: D 1208 ASP cc_start: 0.8022 (t0) cc_final: 0.7801 (p0) REVERT: D 1370 MET cc_start: 0.8735 (ttp) cc_final: 0.8461 (ttm) REVERT: F 219 MET cc_start: 0.8562 (mmt) cc_final: 0.8235 (mmt) REVERT: F 287 TRP cc_start: 0.5850 (t60) cc_final: 0.5533 (t60) REVERT: F 843 MET cc_start: 0.5904 (mmm) cc_final: 0.5397 (mmm) outliers start: 45 outliers final: 19 residues processed: 331 average time/residue: 0.2125 time to fit residues: 116.5447 Evaluate side-chains 280 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 724 ASP Chi-restraints excluded: chain F residue 884 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 117 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 324 optimal weight: 30.0000 chunk 192 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 108 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 387 ASN C1013 GLN F 930 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134281 restraints weight = 47373.682| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.90 r_work: 0.3377 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34520 Z= 0.137 Angle : 0.603 10.879 46868 Z= 0.316 Chirality : 0.044 0.205 5317 Planarity : 0.004 0.074 5999 Dihedral : 10.693 162.975 5104 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 1.77 % Allowed : 12.21 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.12 % 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: -1.37 (0.13), residues: 4165 helix: 0.60 (0.14), residues: 1493 sheet: -0.93 (0.22), residues: 548 loop : -2.08 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 312 TYR 0.016 0.001 TYR C 105 PHE 0.022 0.001 PHE C 804 TRP 0.006 0.001 TRP F 624 HIS 0.006 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (34512) covalent geometry : angle 0.60043 / 0.32 (46856) hydrogen bonds : bond 0.04767 / 3.30 ( 1278) hydrogen bonds : angle 4.68084 / 3.26 ( 3586) metal coordination : bond 0.00739 / 0.44 ( 8) metal coordination : angle 3.50851 / 2.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8067 (p0) cc_final: 0.7830 (p0) REVERT: B 58 GLU cc_start: 0.7868 (tp30) cc_final: 0.7205 (tt0) REVERT: C 151 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7303 (ttt180) REVERT: C 504 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8186 (tm-30) REVERT: C 800 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: C 952 GLN cc_start: 0.8114 (tt0) cc_final: 0.7571 (tm-30) REVERT: C 1304 MET cc_start: 0.8974 (tpp) cc_final: 0.8642 (tpt) REVERT: D 821 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: D 1152 GLU cc_start: 0.7473 (mp0) cc_final: 0.7249 (mp0) REVERT: D 1174 ARG cc_start: 0.7335 (mpt180) cc_final: 0.6716 (mpt180) REVERT: D 1208 ASP cc_start: 0.8027 (t0) cc_final: 0.7176 (m-30) REVERT: D 1370 MET cc_start: 0.8741 (ttp) cc_final: 0.8454 (ttm) REVERT: F 266 LEU cc_start: 0.8061 (tp) cc_final: 0.7290 (mt) REVERT: F 843 MET cc_start: 0.5909 (mmm) cc_final: 0.5506 (mmm) outliers start: 63 outliers final: 27 residues processed: 319 average time/residue: 0.2062 time to fit residues: 109.8475 Evaluate side-chains 291 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 724 ASP Chi-restraints excluded: chain F residue 884 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 271 optimal weight: 10.0000 chunk 413 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** 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 = 0.4284 r_free = 0.4284 target = 0.181715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135109 restraints weight = 47455.148| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.90 r_work: 0.3396 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34520 Z= 0.126 Angle : 0.580 10.553 46868 Z= 0.304 Chirality : 0.043 0.197 5317 Planarity : 0.004 0.069 5999 Dihedral : 10.595 161.568 5104 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 2.08 % Allowed : 12.74 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 4165 helix: 0.84 (0.14), residues: 1489 sheet: -0.85 (0.22), residues: 549 loop : -1.98 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.015 0.001 TYR C 105 PHE 0.025 0.001 PHE D1274 TRP 0.007 0.001 TRP F 624 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (34512) covalent geometry : angle 0.57762 / 0.30 (46856) hydrogen bonds : bond 0.04426 / 3.05 ( 1278) hydrogen bonds : angle 4.50617 / 3.14 ( 3586) metal coordination : bond 0.00670 / 0.40 ( 8) metal coordination : angle 3.17129 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 280 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 58 GLU cc_start: 0.7690 (tp30) cc_final: 0.7290 (tt0) REVERT: C 137 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7990 (t) REVERT: C 151 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7136 (ttt180) REVERT: C 800 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: C 952 GLN cc_start: 0.8010 (tt0) cc_final: 0.7566 (tm-30) REVERT: D 180 MET cc_start: 0.6997 (ttt) cc_final: 0.6710 (ttt) REVERT: D 929 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: D 1152 GLU cc_start: 0.7309 (mp0) cc_final: 0.7064 (mp0) REVERT: D 1208 ASP cc_start: 0.7910 (t0) cc_final: 0.7187 (m-30) REVERT: D 1370 MET cc_start: 0.8769 (ttp) cc_final: 0.8512 (ttm) REVERT: F 266 LEU cc_start: 0.8127 (tp) cc_final: 0.7337 (mt) REVERT: F 287 TRP cc_start: 0.5807 (t60) cc_final: 0.5526 (t60) REVERT: F 589 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5764 (pp) REVERT: F 843 MET cc_start: 0.5931 (mmm) cc_final: 0.5604 (mmm) outliers start: 74 outliers final: 37 residues processed: 336 average time/residue: 0.2093 time to fit residues: 117.7121 Evaluate side-chains 300 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 589 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 724 ASP Chi-restraints excluded: chain F residue 884 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 156 optimal weight: 0.9980 chunk 285 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 233 optimal weight: 0.5980 chunk 408 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 833 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136525 restraints weight = 47379.291| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.95 r_work: 0.3418 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34520 Z= 0.109 Angle : 0.553 10.303 46868 Z= 0.290 Chirality : 0.042 0.196 5317 Planarity : 0.004 0.065 5999 Dihedral : 10.517 160.911 5104 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 1.96 % Allowed : 13.69 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.07 % 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: -0.94 (0.13), residues: 4165 helix: 1.03 (0.14), residues: 1492 sheet: -0.72 (0.23), residues: 549 loop : -1.88 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.013 0.001 TYR C 105 PHE 0.015 0.001 PHE C 804 TRP 0.019 0.001 TRP F 624 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (34512) covalent geometry : angle 0.55133 / 0.29 (46856) hydrogen bonds : bond 0.04033 / 2.78 ( 1278) hydrogen bonds : angle 4.38497 / 3.06 ( 3586) metal coordination : bond 0.00532 / 0.32 ( 8) metal coordination : angle 3.00977 / 1.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 282 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7987 (p0) cc_final: 0.7700 (p0) REVERT: A 95 LYS cc_start: 0.9047 (mppt) cc_final: 0.8588 (mptt) REVERT: B 48 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 58 GLU cc_start: 0.7832 (tp30) cc_final: 0.7347 (mt-10) REVERT: C 46 GLN cc_start: 0.6467 (mm-40) cc_final: 0.6213 (pp30) REVERT: C 137 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8115 (t) REVERT: C 151 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7250 (ttt180) REVERT: C 213 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8803 (mm) REVERT: C 800 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8540 (mtp) REVERT: C 952 GLN cc_start: 0.8061 (tt0) cc_final: 0.7557 (tm-30) REVERT: C 1306 LYS cc_start: 0.8994 (tppp) cc_final: 0.8773 (tttm) REVERT: D 180 MET cc_start: 0.7130 (ttt) cc_final: 0.6874 (ttt) REVERT: D 1143 ASP cc_start: 0.9043 (t70) cc_final: 0.8540 (t0) REVERT: D 1174 ARG cc_start: 0.7330 (mpt180) cc_final: 0.6611 (mmt-90) REVERT: D 1208 ASP cc_start: 0.7955 (t0) cc_final: 0.7182 (m-30) REVERT: D 1370 MET cc_start: 0.8795 (ttp) cc_final: 0.8511 (ttm) REVERT: F 110 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8219 (mttm) REVERT: F 266 LEU cc_start: 0.8090 (tp) cc_final: 0.7308 (mt) REVERT: F 287 TRP cc_start: 0.5910 (t60) cc_final: 0.5638 (t60) REVERT: F 589 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5771 (pp) REVERT: F 843 MET cc_start: 0.5951 (mmm) cc_final: 0.5688 (mmm) outliers start: 70 outliers final: 34 residues processed: 331 average time/residue: 0.2122 time to fit residues: 116.3166 Evaluate side-chains 302 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 589 LEU Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 965 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 384 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 331 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 396 optimal weight: 0.0980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133804 restraints weight = 47630.254| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.94 r_work: 0.3339 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34520 Z= 0.159 Angle : 0.588 10.369 46868 Z= 0.307 Chirality : 0.043 0.221 5317 Planarity : 0.004 0.064 5999 Dihedral : 10.567 161.384 5104 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 2.22 % Allowed : 14.42 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.07 % 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: -0.97 (0.13), residues: 4165 helix: 1.02 (0.14), residues: 1498 sheet: -0.73 (0.22), residues: 558 loop : -1.92 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.014 0.001 TYR C 105 PHE 0.029 0.001 PHE C 804 TRP 0.018 0.001 TRP F 624 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (34512) covalent geometry : angle 0.58647 / 0.31 (46856) hydrogen bonds : bond 0.04577 / 3.15 ( 1278) hydrogen bonds : angle 4.39355 / 3.06 ( 3586) metal coordination : bond 0.00883 / 0.53 ( 8) metal coordination : angle 2.87599 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8032 (p0) cc_final: 0.7821 (p0) REVERT: B 48 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 58 GLU cc_start: 0.7853 (tp30) cc_final: 0.7363 (mt-10) REVERT: C 137 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8243 (t) REVERT: C 151 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7343 (ttt180) REVERT: C 213 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8729 (mm) REVERT: C 498 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6904 (mp) REVERT: C 800 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: C 952 GLN cc_start: 0.8049 (tt0) cc_final: 0.7552 (tm-30) REVERT: D 1025 MET cc_start: 0.3975 (OUTLIER) cc_final: 0.3021 (mtp) REVERT: D 1143 ASP cc_start: 0.9099 (t70) cc_final: 0.8568 (t0) REVERT: D 1174 ARG cc_start: 0.7176 (mpt180) cc_final: 0.6690 (mpt180) REVERT: D 1208 ASP cc_start: 0.8032 (t0) cc_final: 0.7189 (m-30) REVERT: D 1370 MET cc_start: 0.8703 (ttp) cc_final: 0.8438 (ttm) REVERT: F 110 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8220 (mmtt) REVERT: F 219 MET cc_start: 0.8392 (mmt) cc_final: 0.8086 (mmt) REVERT: F 266 LEU cc_start: 0.8063 (tp) cc_final: 0.7290 (mt) REVERT: F 287 TRP cc_start: 0.5958 (t60) cc_final: 0.5692 (t60) REVERT: F 843 MET cc_start: 0.6084 (mmm) cc_final: 0.5860 (mmm) outliers start: 79 outliers final: 55 residues processed: 330 average time/residue: 0.2104 time to fit residues: 115.9171 Evaluate side-chains 324 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 1025 MET Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 337 HIS Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 480 ASP Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 884 VAL Chi-restraints excluded: chain F residue 965 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 281 optimal weight: 40.0000 chunk 173 optimal weight: 0.9990 chunk 250 optimal weight: 0.3980 chunk 243 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134647 restraints weight = 47356.893| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.91 r_work: 0.3384 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34520 Z= 0.133 Angle : 0.570 10.299 46868 Z= 0.298 Chirality : 0.043 0.188 5317 Planarity : 0.004 0.063 5999 Dihedral : 10.561 160.841 5104 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 1.77 % Allowed : 15.10 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.07 % 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: -0.90 (0.13), residues: 4165 helix: 1.08 (0.14), residues: 1502 sheet: -0.69 (0.22), residues: 558 loop : -1.89 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.014 0.001 TYR C 742 PHE 0.024 0.001 PHE D1274 TRP 0.020 0.001 TRP F 624 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (34512) covalent geometry : angle 0.56891 / 0.30 (46856) hydrogen bonds : bond 0.04330 / 2.98 ( 1278) hydrogen bonds : angle 4.32667 / 3.01 ( 3586) metal coordination : bond 0.00721 / 0.44 ( 8) metal coordination : angle 2.71210 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7997 (p0) cc_final: 0.7760 (p0) REVERT: B 48 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 58 GLU cc_start: 0.7901 (tp30) cc_final: 0.7428 (mt-10) REVERT: C 137 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8180 (t) REVERT: C 151 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7345 (ttt180) REVERT: C 213 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8783 (mm) REVERT: C 498 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7022 (mp) REVERT: C 952 GLN cc_start: 0.8068 (tt0) cc_final: 0.7620 (tm-30) REVERT: D 1143 ASP cc_start: 0.9089 (t70) cc_final: 0.8568 (t0) REVERT: D 1208 ASP cc_start: 0.8008 (t0) cc_final: 0.7227 (m-30) REVERT: F 219 MET cc_start: 0.8529 (mmt) cc_final: 0.8237 (mmt) REVERT: F 266 LEU cc_start: 0.8100 (tp) cc_final: 0.7318 (mt) REVERT: F 287 TRP cc_start: 0.5886 (t60) cc_final: 0.5624 (t60) REVERT: F 711 ASP cc_start: 0.8832 (m-30) cc_final: 0.8578 (t70) REVERT: F 843 MET cc_start: 0.6062 (mmm) cc_final: 0.5855 (mmm) outliers start: 63 outliers final: 48 residues processed: 317 average time/residue: 0.2015 time to fit residues: 106.8483 Evaluate side-chains 315 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 54 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 884 VAL Chi-restraints excluded: chain F residue 965 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 361 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 227 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 320 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137183 restraints weight = 47375.590| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.88 r_work: 0.3428 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34520 Z= 0.105 Angle : 0.563 18.323 46868 Z= 0.290 Chirality : 0.042 0.219 5317 Planarity : 0.004 0.060 5999 Dihedral : 10.507 160.105 5104 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.60 % Allowed : 15.35 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.05 % 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: -0.72 (0.13), residues: 4165 helix: 1.24 (0.14), residues: 1495 sheet: -0.57 (0.23), residues: 554 loop : -1.78 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.012 0.001 TYR D 679 PHE 0.012 0.001 PHE D1037 TRP 0.022 0.001 TRP F 624 HIS 0.006 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (34512) covalent geometry : angle 0.56159 / 0.29 (46856) hydrogen bonds : bond 0.03809 / 2.62 ( 1278) hydrogen bonds : angle 4.21933 / 2.93 ( 3586) metal coordination : bond 0.00421 / 0.25 ( 8) metal coordination : angle 2.70289 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7998 (p0) cc_final: 0.7764 (p0) REVERT: A 95 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8526 (mptt) REVERT: B 58 GLU cc_start: 0.7904 (tp30) cc_final: 0.7485 (tt0) REVERT: C 36 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8564 (tp40) REVERT: C 151 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7260 (ttt180) REVERT: C 213 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8728 (mm) REVERT: C 498 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6909 (mp) REVERT: C 952 GLN cc_start: 0.7977 (tt0) cc_final: 0.7587 (tm-30) REVERT: D 1143 ASP cc_start: 0.9071 (t70) cc_final: 0.8587 (t0) REVERT: D 1174 ARG cc_start: 0.7467 (mpt180) cc_final: 0.6569 (mpt180) REVERT: D 1208 ASP cc_start: 0.7965 (t0) cc_final: 0.7178 (m-30) REVERT: F 219 MET cc_start: 0.8442 (mmt) cc_final: 0.8122 (mmt) REVERT: F 266 LEU cc_start: 0.8055 (tp) cc_final: 0.7279 (mt) REVERT: F 287 TRP cc_start: 0.5867 (t60) cc_final: 0.5590 (t60) REVERT: F 711 ASP cc_start: 0.8856 (m-30) cc_final: 0.8599 (t70) REVERT: F 843 MET cc_start: 0.6104 (mmm) cc_final: 0.5896 (mmm) outliers start: 57 outliers final: 39 residues processed: 321 average time/residue: 0.2114 time to fit residues: 112.3663 Evaluate side-chains 308 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain F residue 884 VAL Chi-restraints excluded: chain F residue 965 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 142 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 194 GLN B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.178542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131455 restraints weight = 47903.209| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.99 r_work: 0.3344 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34520 Z= 0.213 Angle : 0.642 10.339 46868 Z= 0.334 Chirality : 0.045 0.207 5317 Planarity : 0.005 0.118 5999 Dihedral : 10.623 161.281 5104 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.47 % Rotamer: Outliers : 1.54 % Allowed : 15.46 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.07 % 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: -0.91 (0.13), residues: 4165 helix: 1.06 (0.14), residues: 1509 sheet: -0.68 (0.22), residues: 557 loop : -1.91 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 114 TYR 0.015 0.001 TYR C 742 PHE 0.036 0.002 PHE C 804 TRP 0.019 0.001 TRP F 624 HIS 0.007 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.21 (34512) covalent geometry : angle 0.64040 / 0.33 (46856) hydrogen bonds : bond 0.05044 / 3.46 ( 1278) hydrogen bonds : angle 4.38146 / 3.05 ( 3586) metal coordination : bond 0.01230 / 0.75 ( 8) metal coordination : angle 2.84937 / 1.74 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8330 Ramachandran restraints generated. 4165 Oldfield, 0 Emsley, 4165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8602 (mptt) REVERT: B 58 GLU cc_start: 0.7802 (tp30) cc_final: 0.7397 (tt0) REVERT: C 151 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7255 (ttt180) REVERT: C 213 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8822 (mm) REVERT: C 490 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7942 (tp40) REVERT: C 498 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6963 (mp) REVERT: C 804 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7124 (p90) REVERT: C 952 GLN cc_start: 0.8023 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 1143 ASP cc_start: 0.9034 (t70) cc_final: 0.8450 (t0) REVERT: D 1208 ASP cc_start: 0.7891 (t0) cc_final: 0.7195 (m-30) REVERT: F 219 MET cc_start: 0.8423 (mmt) cc_final: 0.8135 (mmt) REVERT: F 266 LEU cc_start: 0.8137 (tp) cc_final: 0.7354 (mt) REVERT: F 287 TRP cc_start: 0.5888 (t60) cc_final: 0.5614 (t60) REVERT: F 711 ASP cc_start: 0.8784 (m-30) cc_final: 0.8544 (t70) REVERT: F 843 MET cc_start: 0.6105 (mmm) cc_final: 0.5815 (mmm) outliers start: 55 outliers final: 44 residues processed: 308 average time/residue: 0.2050 time to fit residues: 104.1722 Evaluate side-chains 307 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1005 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain F residue 884 VAL Chi-restraints excluded: chain F residue 965 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 143 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 368 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 194 GLN B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133627 restraints weight = 47499.042| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.90 r_work: 0.3336 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34520 Z= 0.147 Angle : 0.592 10.245 46868 Z= 0.309 Chirality : 0.043 0.180 5317 Planarity : 0.004 0.060 5999 Dihedral : 10.596 160.556 5104 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.69 % Favored : 94.29 % Rotamer: Outliers : 1.54 % Allowed : 15.66 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4165 helix: 1.10 (0.14), residues: 1513 sheet: -0.63 (0.23), residues: 554 loop : -1.87 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 359 TYR 0.014 0.001 TYR C 742 PHE 0.020 0.001 PHE C 804 TRP 0.022 0.001 TRP F 624 HIS 0.006 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (34512) covalent geometry : angle 0.59035 / 0.31 (46856) hydrogen bonds : bond 0.04509 / 3.10 ( 1278) hydrogen bonds : angle 4.31176 / 2.99 ( 3586) metal coordination : bond 0.00778 / 0.48 ( 8) metal coordination : angle 2.66649 / 1.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9043.76 seconds wall clock time: 155 minutes 21.38 seconds (9321.38 seconds total)