Starting phenix.real_space_refine on Tue Sep 15 10:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.map" model { file = "/net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1k_22625/09_2026/7k1k_22625.cif" } resolution = 4.1 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 71 5.49 5 S 224 5.16 5 C 24290 2.51 5 N 6514 2.21 5 O 7144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38243 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 28577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3604, 28577 Classifications: {'peptide': 3604} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 148, 'TRANS': 3454} Chain breaks: 20 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 33, 'ASP:plan': 1, 'ARG:plan': 4, 'PHE:plan': 3, 'HIS:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 229 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3954 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4204 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 7.26, per 1000 atoms: 0.19 Number of scatterers: 38243 At special positions: 0 Unit cell: (133.4, 164.72, 240.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 224 16.00 P 71 15.00 O 7144 8.00 N 6514 7.00 C 24290 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8856 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 14 sheets defined 58.4% alpha, 4.3% beta 33 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 25 through 42 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.831A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 96 removed outlier: 4.310A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Proline residue: A 102 - end of helix Processing helix chain 'A' and resid 103 through 118 removed outlier: 4.059A pdb=" N ILE A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.824A pdb=" N ALA A 127 " --> pdb=" O CYS A 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.109A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.524A pdb=" N LYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 removed outlier: 3.659A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.077A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.636A pdb=" N HIS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.000A pdb=" N LYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 4.764A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.862A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.282A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.931A pdb=" N CYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.880A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.936A pdb=" N GLN A 539 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.813A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.953A pdb=" N GLU A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 646 through 660 Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 701 through 718 removed outlier: 4.067A pdb=" N VAL A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.189A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.630A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 847 through 863 removed outlier: 3.769A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 removed outlier: 3.552A pdb=" N ASN A 869 " --> pdb=" O ILE A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 4.443A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 945 removed outlier: 4.021A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 974 Proline residue: A 967 - end of helix removed outlier: 4.187A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 removed outlier: 3.727A pdb=" N ILE A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 removed outlier: 3.711A pdb=" N PHE A1001 " --> pdb=" O ASN A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'A' and resid 1025 through 1043 removed outlier: 4.303A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A1043 " --> pdb=" O TRP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 4.203A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1114 Processing helix chain 'A' and resid 1123 through 1139 removed outlier: 3.819A pdb=" N LEU A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 4.084A pdb=" N ARG A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1226 removed outlier: 3.956A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N SER A1218 " --> pdb=" O GLU A1214 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A1219 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A1223 " --> pdb=" O PHE A1219 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1273 removed outlier: 3.805A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A1270 " --> pdb=" O CYS A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.961A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1298 Processing helix chain 'A' and resid 1325 through 1351 removed outlier: 3.969A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1365 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.493A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1382 removed outlier: 3.898A pdb=" N SER A1381 " --> pdb=" O GLU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1405 Proline residue: A1396 - end of helix removed outlier: 3.936A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 removed outlier: 3.946A pdb=" N LEU A1415 " --> pdb=" O TYR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1431 removed outlier: 3.762A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1461 removed outlier: 4.469A pdb=" N ARG A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.731A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1518 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.641A pdb=" N LEU A1533 " --> pdb=" O VAL A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1563 removed outlier: 3.703A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1577 through 1584 Processing helix chain 'A' and resid 1589 through 1605 removed outlier: 4.260A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1623 Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing helix chain 'A' and resid 1642 through 1655 Processing helix chain 'A' and resid 1667 through 1679 Processing helix chain 'A' and resid 1689 through 1694 Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1735 through 1753 Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 4.249A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.995A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1807 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.824A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1830 removed outlier: 3.754A pdb=" N LEU A1827 " --> pdb=" O SER A1823 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 4.395A pdb=" N ALA A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 3.879A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1910 through 1922 removed outlier: 3.507A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1955 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.755A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2016 Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.538A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2126 through 2134 removed outlier: 3.629A pdb=" N GLY A2134 " --> pdb=" O HIS A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.715A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A2152 " --> pdb=" O LYS A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2174 removed outlier: 3.887A pdb=" N ALA A2172 " --> pdb=" O LEU A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2194 Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 3.659A pdb=" N VAL A2210 " --> pdb=" O PRO A2206 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 3.708A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A2232 " --> pdb=" O ARG A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2260 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.942A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 4.150A pdb=" N TYR A2299 " --> pdb=" O GLN A2295 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2333 Processing helix chain 'A' and resid 2337 through 2356 removed outlier: 4.387A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A2343 " --> pdb=" O GLU A2339 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 Processing helix chain 'A' and resid 2378 through 2385 Processing helix chain 'A' and resid 2390 through 2403 removed outlier: 3.535A pdb=" N LYS A2394 " --> pdb=" O HIS A2390 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS A2403 " --> pdb=" O GLU A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 removed outlier: 3.747A pdb=" N LEU A2415 " --> pdb=" O LEU A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.714A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 removed outlier: 3.893A pdb=" N GLN A2432 " --> pdb=" O ASP A2428 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A2441 " --> pdb=" O ASP A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2455 removed outlier: 4.436A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2457 through 2461 removed outlier: 3.815A pdb=" N GLU A2460 " --> pdb=" O PRO A2457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A2461 " --> pdb=" O VAL A2458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2457 through 2461' Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.509A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2504 Processing helix chain 'A' and resid 2504 through 2509 removed outlier: 3.614A pdb=" N GLN A2508 " --> pdb=" O ASP A2504 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 removed outlier: 3.631A pdb=" N ILE A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2542 removed outlier: 4.472A pdb=" N LEU A2539 " --> pdb=" O THR A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.167A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2799 removed outlier: 4.475A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.607A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.799A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2862 removed outlier: 4.381A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) Processing helix chain 'A' and resid 2875 through 2881 Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.780A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2931 Processing helix chain 'A' and resid 2937 through 2943 removed outlier: 3.923A pdb=" N ILE A2942 " --> pdb=" O VAL A2938 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A2943 " --> pdb=" O LEU A2939 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 4.400A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2966 through 2971 Processing helix chain 'A' and resid 2972 through 2977 removed outlier: 4.135A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3004 removed outlier: 3.775A pdb=" N LYS A2991 " --> pdb=" O THR A2987 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A2992 " --> pdb=" O GLU A2988 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A2995 " --> pdb=" O LYS A2991 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3017 removed outlier: 4.390A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 4.100A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3053 removed outlier: 4.409A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3069 Processing helix chain 'A' and resid 3071 through 3076 Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 4.016A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3154 through 3167 removed outlier: 3.680A pdb=" N ARG A3167 " --> pdb=" O THR A3163 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.797A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A3197 " --> pdb=" O ILE A3193 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3247 Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 3.739A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 3.724A pdb=" N LEU A3273 " --> pdb=" O ARG A3269 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A3289 " --> pdb=" O HIS A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3302 removed outlier: 4.443A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3314 through 3319 removed outlier: 3.518A pdb=" N LYS A3318 " --> pdb=" O SER A3314 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A3319 " --> pdb=" O TYR A3315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3314 through 3319' Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 3.634A pdb=" N LEU A3341 " --> pdb=" O ILE A3337 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A3343 " --> pdb=" O ASN A3339 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.849A pdb=" N ALA A3349 " --> pdb=" O ALA A3346 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A3351 " --> pdb=" O LEU A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3362 removed outlier: 3.613A pdb=" N LEU A3362 " --> pdb=" O ARG A3358 " (cutoff:3.500A) Processing helix chain 'A' and resid 3373 through 3389 removed outlier: 3.681A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3427 removed outlier: 3.903A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3455 removed outlier: 3.665A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 removed outlier: 3.997A pdb=" N LEU A3463 " --> pdb=" O ASN A3459 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3475 removed outlier: 3.758A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3488 removed outlier: 4.267A pdb=" N MET A3483 " --> pdb=" O THR A3479 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3502 removed outlier: 3.913A pdb=" N ILE A3499 " --> pdb=" O ILE A3496 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 4.184A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3562 removed outlier: 3.538A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3596 removed outlier: 3.779A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3617 removed outlier: 4.365A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3643 through 3651 Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 3.533A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3689 removed outlier: 3.923A pdb=" N SER A3688 " --> pdb=" O SER A3684 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A3689 " --> pdb=" O PRO A3685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3684 through 3689' Processing helix chain 'A' and resid 3712 through 3716 removed outlier: 3.696A pdb=" N TYR A3715 " --> pdb=" O LEU A3712 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A3716 " --> pdb=" O PRO A3713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3712 through 3716' Processing helix chain 'A' and resid 3759 through 3775 Processing helix chain 'A' and resid 3778 through 3783 removed outlier: 3.901A pdb=" N SER A3782 " --> pdb=" O ASP A3778 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 3.913A pdb=" N LYS A3825 " --> pdb=" O SER A3821 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 Processing helix chain 'A' and resid 3854 through 3861 removed outlier: 4.219A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3876 removed outlier: 3.735A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3889 Processing helix chain 'A' and resid 3895 through 3915 removed outlier: 4.475A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3948 through 3953 removed outlier: 3.979A pdb=" N PHE A3952 " --> pdb=" O SER A3948 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3948 through 3953' Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3996 through 4007 removed outlier: 3.587A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4023 removed outlier: 4.069A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4042 through 4053 Processing helix chain 'A' and resid 4057 through 4066 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.586A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.738A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 removed outlier: 3.554A pdb=" N GLU A4125 " --> pdb=" O GLU A4122 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 75 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 143 through 155 removed outlier: 4.250A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 removed outlier: 4.074A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.317A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.664A pdb=" N LEU B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.766A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 48 removed outlier: 4.052A pdb=" N GLN C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 removed outlier: 4.308A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 removed outlier: 4.159A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 198 through 216 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 4.369A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.991A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 4.216A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.820A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 removed outlier: 3.568A pdb=" N MET A3929 " --> pdb=" O ILE A3938 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.018A pdb=" N ASP B 36 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 42 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 removed outlier: 4.034A pdb=" N LEU B 366 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 434 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU B 345 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS B 260 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU B 347 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYS B 262 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY B 349 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.375A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS C 131 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 253 removed outlier: 3.578A pdb=" N ALA C 366 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE C 340 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 252 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.641A pdb=" N LEU C 297 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 314 through 316 Processing sheet with id=AB5, first strand: chain 'C' and resid 464 through 466 1682 hydrogen bonds defined for protein. 4905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 13.50 Time building geometry restraints manager: 4.14 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: 9379 1.33 - 1.45: 8246 1.45 - 1.58: 21043 1.58 - 1.70: 141 1.70 - 1.82: 352 Bond restraints: 39161 Sorted by residual: bond pdb=" C ASN A2456 " pdb=" N PRO A2457 " ideal model delta sigma weight residual 1.332 1.366 -0.034 8.20e-03 1.49e+04 1.72e+01 bond pdb=" C4' DA G 25 " pdb=" C3' DA G 25 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.00e-02 1.00e+04 1.45e+01 bond pdb=" N ARG B 244 " pdb=" CA ARG B 244 " ideal model delta sigma weight residual 1.459 1.493 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" C3' DC G 28 " pdb=" C2' DC G 28 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C1' DC F 17 " pdb=" N1 DC F 17 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 ... (remaining 39156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 52176 3.31 - 6.61: 899 6.61 - 9.92: 139 9.92 - 13.23: 15 13.23 - 16.53: 6 Bond angle restraints: 53235 Sorted by residual: angle pdb=" C GLU A3344 " pdb=" N PRO A3345 " pdb=" CA PRO A3345 " ideal model delta sigma weight residual 119.84 135.92 -16.08 1.25e+00 6.40e-01 1.66e+02 angle pdb=" N THR A1473 " pdb=" CA THR A1473 " pdb=" C THR A1473 " ideal model delta sigma weight residual 110.80 97.81 12.99 2.13e+00 2.20e-01 3.72e+01 angle pdb=" N SER B 475 " pdb=" CA SER B 475 " pdb=" C SER B 475 " ideal model delta sigma weight residual 114.75 107.07 7.68 1.26e+00 6.30e-01 3.72e+01 angle pdb=" O4' DA G 25 " pdb=" C4' DA G 25 " pdb=" C3' DA G 25 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" CA VAL A1845 " pdb=" C VAL A1845 " pdb=" N ASP A1846 " ideal model delta sigma weight residual 116.60 124.63 -8.03 1.45e+00 4.76e-01 3.07e+01 ... (remaining 53230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 20067 17.80 - 35.60: 2756 35.60 - 53.40: 708 53.40 - 71.20: 156 71.20 - 89.00: 30 Dihedral angle restraints: 23717 sinusoidal: 10133 harmonic: 13584 Sorted by residual: dihedral pdb=" CD ARG B 244 " pdb=" NE ARG B 244 " pdb=" CZ ARG B 244 " pdb=" NH1 ARG B 244 " ideal model delta sinusoidal sigma weight residual 0.00 -83.07 83.07 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CD ARG A 213 " pdb=" NE ARG A 213 " pdb=" CZ ARG A 213 " pdb=" NH1 ARG A 213 " ideal model delta sinusoidal sigma weight residual 0.00 -74.02 74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA GLN A 638 " pdb=" C GLN A 638 " pdb=" N ALA A 639 " pdb=" CA ALA A 639 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 23714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4534 0.066 - 0.131: 1300 0.131 - 0.197: 192 0.197 - 0.263: 33 0.263 - 0.329: 3 Chirality restraints: 6062 Sorted by residual: chirality pdb=" CB ILE A2251 " pdb=" CA ILE A2251 " pdb=" CG1 ILE A2251 " pdb=" CG2 ILE A2251 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA THR A1473 " pdb=" N THR A1473 " pdb=" C THR A1473 " pdb=" CB THR A1473 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ASP A2486 " pdb=" N ASP A2486 " pdb=" C ASP A2486 " pdb=" CB ASP A2486 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 6059 not shown) Planarity restraints: 6507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 244 " -1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG B 244 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 244 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 244 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 244 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 1.055 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG A 213 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A3344 " 0.022 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C GLU A3344 " -0.079 2.00e-02 2.50e+03 pdb=" O GLU A3344 " 0.030 2.00e-02 2.50e+03 pdb=" N PRO A3345 " 0.027 2.00e-02 2.50e+03 ... (remaining 6504 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6518 2.76 - 3.29: 36212 3.29 - 3.83: 61036 3.83 - 4.36: 68093 4.36 - 4.90: 113418 Nonbonded interactions: 285277 Sorted by model distance: nonbonded pdb=" OH TYR B 141 " pdb=" OE2 GLU B 172 " model vdw 2.224 3.040 nonbonded pdb=" O GLN A1963 " pdb=" OG SER A1968 " model vdw 2.240 3.040 nonbonded pdb=" OG SER A 75 " pdb=" OE1 GLU A 77 " model vdw 2.249 3.040 nonbonded pdb=" O GLN A 409 " pdb=" OG SER A 412 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 298 " pdb=" O VAL C 294 " model vdw 2.255 3.040 ... (remaining 285272 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 'D' and resid 4 through 24) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 42.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.008 0.096 39161 Z= 0.392 Angle : 1.129 16.534 53235 Z= 0.634 Chirality : 0.061 0.329 6062 Planarity : 0.012 0.489 6507 Dihedral : 17.537 89.002 14861 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.05 % Favored : 85.54 % Rotamer: Outliers : 0.91 % Allowed : 12.93 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.07 (0.09), residues: 4570 helix: -2.96 (0.07), residues: 2526 sheet: -1.85 (0.33), residues: 217 loop : -4.06 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 354 TYR 0.024 0.003 TYR A 682 PHE 0.042 0.003 PHE A1923 TRP 0.035 0.003 TRP A2981 HIS 0.012 0.002 HIS A3004 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.39 (39161) covalent geometry : angle 1.12943 / 0.63 (53235) hydrogen bonds : bond 0.11196 / 7.45 ( 1763) hydrogen bonds : angle 6.42679 / 4.51 ( 5067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 552 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6019 (tpt) cc_final: 0.5689 (tpp) REVERT: A 1127 CYS cc_start: 0.7782 (p) cc_final: 0.6836 (t) REVERT: A 1213 LYS cc_start: 0.8495 (pptt) cc_final: 0.7699 (mttt) REVERT: A 1592 MET cc_start: 0.6083 (tpp) cc_final: 0.5513 (tpp) REVERT: A 1739 TYR cc_start: 0.6654 (t80) cc_final: 0.6322 (t80) REVERT: A 1773 VAL cc_start: 0.4939 (OUTLIER) cc_final: 0.4561 (m) REVERT: A 1774 MET cc_start: 0.5740 (mmp) cc_final: 0.5496 (mmm) REVERT: A 2236 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 2281 MET cc_start: 0.7243 (tpt) cc_final: 0.7007 (tpt) REVERT: A 2299 TYR cc_start: 0.6950 (t80) cc_final: 0.6564 (t80) REVERT: A 2473 MET cc_start: 0.8720 (ttt) cc_final: 0.8500 (ttt) REVERT: A 2820 MET cc_start: 0.7789 (ppp) cc_final: 0.7468 (ppp) REVERT: A 3001 CYS cc_start: 0.7871 (m) cc_final: 0.7545 (t) REVERT: A 3609 MET cc_start: 0.7728 (ptm) cc_final: 0.7477 (tmm) REVERT: A 3628 PHE cc_start: 0.5525 (m-10) cc_final: 0.5293 (m-10) REVERT: A 3808 ASN cc_start: 0.8078 (t0) cc_final: 0.7808 (p0) REVERT: A 3918 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 145 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 403 ARG cc_start: 0.8366 (ptp90) cc_final: 0.8083 (mtm110) REVERT: B 480 ASN cc_start: 0.7410 (t0) cc_final: 0.7205 (t0) REVERT: C 115 MET cc_start: 0.7270 (tpt) cc_final: 0.6861 (tpt) REVERT: C 302 GLU cc_start: 0.7423 (mp0) cc_final: 0.7196 (mt-10) outliers start: 37 outliers final: 18 residues processed: 587 average time/residue: 0.2329 time to fit residues: 221.6430 Evaluate side-chains 392 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 372 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.3980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 32 HIS A 377 ASN A 613 HIS A 982 GLN A1083 ASN A1126 GLN A1654 GLN A1771 GLN A1890 HIS A1932 GLN A1941 HIS A1957 ASN ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2089 ASN A2130 HIS A2222 HIS ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2352 HIS A2365 ASN A2464 HIS A2496 GLN A2831 ASN A3084 GLN A3130 GLN A3327 ASN A3390 GLN A3501 HIS ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3569 GLN A3573 ASN A3634 GLN A3716 HIS A3772 ASN A4032 ASN A4055 ASN B 65 GLN B 68 GLN B 98 ASN B 416 GLN B 426 GLN B 433 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 76 ASN C 80 HIS C 119 GLN C 330 GLN C 509 GLN C 517 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108742 restraints weight = 112589.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107569 restraints weight = 154121.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108458 restraints weight = 131901.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109172 restraints weight = 89441.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109305 restraints weight = 81894.992| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39161 Z= 0.157 Angle : 0.759 13.205 53235 Z= 0.395 Chirality : 0.045 0.200 6062 Planarity : 0.006 0.077 6507 Dihedral : 14.181 65.511 5750 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.86 % Favored : 88.01 % Rotamer: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.83 (0.11), residues: 4570 helix: -1.71 (0.09), residues: 2540 sheet: -1.66 (0.34), residues: 218 loop : -3.86 (0.12), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A2090 TYR 0.024 0.002 TYR B 530 PHE 0.040 0.002 PHE C 323 TRP 0.026 0.001 TRP A2981 HIS 0.010 0.001 HIS A1772 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (39161) covalent geometry : angle 0.75862 / 0.40 (53235) hydrogen bonds : bond 0.04781 / 3.12 ( 1763) hydrogen bonds : angle 5.37080 / 3.78 ( 5067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 522 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.5741 (tpt) cc_final: 0.5481 (tpt) REVERT: A 1124 ILE cc_start: 0.8226 (pt) cc_final: 0.7793 (pt) REVERT: A 1127 CYS cc_start: 0.7509 (p) cc_final: 0.7246 (m) REVERT: A 1213 LYS cc_start: 0.8668 (pptt) cc_final: 0.7908 (mttt) REVERT: A 1739 TYR cc_start: 0.6685 (t80) cc_final: 0.6272 (t80) REVERT: A 1774 MET cc_start: 0.6398 (mmp) cc_final: 0.5998 (mmm) REVERT: A 1927 MET cc_start: 0.7128 (mtt) cc_final: 0.6811 (mtm) REVERT: A 2274 ILE cc_start: 0.7529 (pt) cc_final: 0.7260 (pt) REVERT: A 2281 MET cc_start: 0.7070 (tpt) cc_final: 0.6775 (tpt) REVERT: A 2928 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8056 (tttp) REVERT: A 3084 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6880 (tm130) REVERT: A 3181 ASP cc_start: 0.7671 (m-30) cc_final: 0.7409 (m-30) REVERT: A 3535 ILE cc_start: 0.7077 (mt) cc_final: 0.6842 (mt) REVERT: A 3659 PHE cc_start: 0.5617 (m-80) cc_final: 0.5359 (m-10) REVERT: A 3808 ASN cc_start: 0.8017 (t0) cc_final: 0.7697 (p0) REVERT: A 3959 MET cc_start: 0.8976 (pmm) cc_final: 0.8648 (pmm) REVERT: B 163 HIS cc_start: 0.6948 (m90) cc_final: 0.6601 (m90) REVERT: C 115 MET cc_start: 0.7417 (tpt) cc_final: 0.7052 (tpt) REVERT: C 280 ASP cc_start: 0.4953 (p0) cc_final: 0.3972 (t70) outliers start: 4 outliers final: 0 residues processed: 526 average time/residue: 0.2106 time to fit residues: 186.1139 Evaluate side-chains 381 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 335 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 406 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 462 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1465 HIS ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN A2414 GLN A2464 HIS A3081 HIS ** A3084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3510 GLN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN ** A4103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4110 GLN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105057 restraints weight = 113383.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103864 restraints weight = 161582.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104717 restraints weight = 148428.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105683 restraints weight = 97220.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105816 restraints weight = 88588.848| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 39161 Z= 0.277 Angle : 0.847 11.852 53235 Z= 0.441 Chirality : 0.049 0.267 6062 Planarity : 0.006 0.073 6507 Dihedral : 14.168 68.776 5750 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.33 % Favored : 85.51 % Rotamer: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.11), residues: 4570 helix: -1.43 (0.09), residues: 2553 sheet: -1.99 (0.33), residues: 230 loop : -3.76 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2090 TYR 0.031 0.002 TYR A3114 PHE 0.038 0.003 PHE C 491 TRP 0.028 0.002 TRP A2981 HIS 0.013 0.002 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 (39161) covalent geometry : angle 0.84738 / 0.44 (53235) hydrogen bonds : bond 0.05271 / 3.48 ( 1763) hydrogen bonds : angle 5.54941 / 3.91 ( 5067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 475 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.5027 (mmp) cc_final: 0.4807 (mmt) REVERT: A 441 MET cc_start: 0.6013 (tpt) cc_final: 0.5750 (tpt) REVERT: A 994 TRP cc_start: 0.5669 (t-100) cc_final: 0.4515 (m-10) REVERT: A 1124 ILE cc_start: 0.8313 (pt) cc_final: 0.7876 (pt) REVERT: A 1127 CYS cc_start: 0.7777 (p) cc_final: 0.7348 (m) REVERT: A 1213 LYS cc_start: 0.8625 (pptt) cc_final: 0.7874 (mttt) REVERT: A 1583 MET cc_start: 0.8452 (tmm) cc_final: 0.8248 (tmm) REVERT: A 1739 TYR cc_start: 0.6771 (t80) cc_final: 0.6446 (t80) REVERT: A 1871 MET cc_start: 0.8328 (ttm) cc_final: 0.8023 (ttm) REVERT: A 2231 PHE cc_start: 0.7170 (t80) cc_final: 0.6932 (t80) REVERT: A 2281 MET cc_start: 0.7242 (tpt) cc_final: 0.6972 (tpt) REVERT: A 2928 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8188 (tttp) REVERT: A 3181 ASP cc_start: 0.8077 (m-30) cc_final: 0.7868 (m-30) REVERT: A 3450 MET cc_start: 0.7543 (ttt) cc_final: 0.7271 (ttt) REVERT: A 3800 LEU cc_start: 0.6168 (mt) cc_final: 0.5681 (mp) REVERT: A 3808 ASN cc_start: 0.8180 (t0) cc_final: 0.7686 (p0) REVERT: B 163 HIS cc_start: 0.7095 (m90) cc_final: 0.6672 (m90) REVERT: C 84 MET cc_start: 0.7106 (mpp) cc_final: 0.6642 (mpp) REVERT: C 115 MET cc_start: 0.7518 (tpt) cc_final: 0.7140 (tpt) REVERT: C 267 ILE cc_start: 0.8117 (pt) cc_final: 0.7878 (pt) outliers start: 5 outliers final: 4 residues processed: 480 average time/residue: 0.2167 time to fit residues: 175.1953 Evaluate side-chains 356 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 352 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 325 optimal weight: 0.5980 chunk 353 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 298 optimal weight: 0.0370 chunk 106 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2352 HIS A2365 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3716 HIS A4110 GLN B 158 GLN B 176 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.127842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109308 restraints weight = 111160.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109126 restraints weight = 115688.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109525 restraints weight = 101675.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110550 restraints weight = 77258.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110600 restraints weight = 63208.790| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39161 Z= 0.136 Angle : 0.706 11.536 53235 Z= 0.365 Chirality : 0.044 0.178 6062 Planarity : 0.005 0.075 6507 Dihedral : 13.867 66.229 5750 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.42 % Favored : 88.47 % Rotamer: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.12), residues: 4570 helix: -0.95 (0.10), residues: 2543 sheet: -1.42 (0.36), residues: 194 loop : -3.61 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG A 70 TYR 0.022 0.001 TYR A1940 PHE 0.033 0.002 PHE C 491 TRP 0.032 0.002 TRP A1356 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (39161) covalent geometry : angle 0.70645 / 0.36 (53235) hydrogen bonds : bond 0.04182 / 2.72 ( 1763) hydrogen bonds : angle 4.97923 / 3.50 ( 5067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6600 (pp) REVERT: A 208 MET cc_start: 0.8078 (tpt) cc_final: 0.7085 (tpp) REVERT: A 441 MET cc_start: 0.5817 (tpt) cc_final: 0.5549 (tpt) REVERT: A 994 TRP cc_start: 0.5255 (t-100) cc_final: 0.4207 (m-10) REVERT: A 1127 CYS cc_start: 0.7605 (p) cc_final: 0.7306 (m) REVERT: A 1213 LYS cc_start: 0.8579 (pptt) cc_final: 0.7843 (mttt) REVERT: A 1583 MET cc_start: 0.8377 (tmm) cc_final: 0.7916 (tmm) REVERT: A 1592 MET cc_start: 0.6203 (tpp) cc_final: 0.5372 (tpp) REVERT: A 1739 TYR cc_start: 0.6673 (t80) cc_final: 0.5973 (t80) REVERT: A 1743 MET cc_start: 0.7811 (mmp) cc_final: 0.7426 (mmm) REVERT: A 1949 ILE cc_start: 0.8657 (mm) cc_final: 0.8365 (mm) REVERT: A 2171 LEU cc_start: 0.8101 (tt) cc_final: 0.7868 (tp) REVERT: A 2274 ILE cc_start: 0.7603 (pt) cc_final: 0.7351 (pt) REVERT: A 2281 MET cc_start: 0.7191 (tpt) cc_final: 0.6910 (tpt) REVERT: A 2410 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 2928 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7951 (tttp) REVERT: A 3123 GLN cc_start: 0.7904 (tt0) cc_final: 0.7677 (tt0) REVERT: A 3260 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6453 (tppt) REVERT: A 3535 ILE cc_start: 0.7463 (mt) cc_final: 0.7133 (mt) REVERT: A 3808 ASN cc_start: 0.8088 (t0) cc_final: 0.7739 (p0) REVERT: B 68 GLN cc_start: 0.7020 (mt0) cc_final: 0.6780 (mt0) REVERT: B 163 HIS cc_start: 0.6733 (m90) cc_final: 0.6379 (m90) REVERT: C 115 MET cc_start: 0.7164 (tpt) cc_final: 0.6898 (tpt) outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.2136 time to fit residues: 189.6020 Evaluate side-chains 381 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 27 optimal weight: 8.9990 chunk 381 optimal weight: 9.9990 chunk 219 optimal weight: 0.0570 chunk 261 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS A 998 ASN ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN A2865 HIS A3339 ASN A3510 GLN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108730 restraints weight = 110663.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107622 restraints weight = 135666.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108502 restraints weight = 119138.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108959 restraints weight = 82382.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109075 restraints weight = 78424.125| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39161 Z= 0.137 Angle : 0.685 12.461 53235 Z= 0.355 Chirality : 0.043 0.187 6062 Planarity : 0.005 0.070 6507 Dihedral : 13.751 64.805 5750 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.04 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.12), residues: 4570 helix: -0.75 (0.10), residues: 2551 sheet: -1.38 (0.35), residues: 194 loop : -3.54 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.021 0.001 TYR A2299 PHE 0.038 0.002 PHE C 491 TRP 0.016 0.001 TRP A2981 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (39161) covalent geometry : angle 0.68529 / 0.36 (53235) hydrogen bonds : bond 0.04002 / 2.62 ( 1763) hydrogen bonds : angle 4.86734 / 3.42 ( 5067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8112 (tpt) cc_final: 0.7070 (tpp) REVERT: A 441 MET cc_start: 0.5894 (tpt) cc_final: 0.5560 (tpt) REVERT: A 994 TRP cc_start: 0.5248 (t-100) cc_final: 0.4382 (m-10) REVERT: A 1124 ILE cc_start: 0.8112 (pt) cc_final: 0.7653 (pt) REVERT: A 1127 CYS cc_start: 0.7606 (p) cc_final: 0.7242 (m) REVERT: A 1213 LYS cc_start: 0.8637 (pptt) cc_final: 0.7941 (mttt) REVERT: A 1583 MET cc_start: 0.8456 (tmm) cc_final: 0.7985 (tmm) REVERT: A 1739 TYR cc_start: 0.6883 (t80) cc_final: 0.6167 (t80) REVERT: A 1743 MET cc_start: 0.7956 (mmp) cc_final: 0.7522 (mmm) REVERT: A 1949 ILE cc_start: 0.8684 (mm) cc_final: 0.8386 (mm) REVERT: A 1986 ARG cc_start: 0.7027 (ptt-90) cc_final: 0.6756 (ptt90) REVERT: A 2002 LYS cc_start: 0.8077 (mppt) cc_final: 0.7566 (mppt) REVERT: A 2281 MET cc_start: 0.7031 (tpt) cc_final: 0.6606 (tpt) REVERT: A 2928 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8055 (tttp) REVERT: A 3256 MET cc_start: 0.7917 (tpp) cc_final: 0.7625 (tpt) REVERT: A 3260 LYS cc_start: 0.6965 (mmtt) cc_final: 0.6574 (tppt) REVERT: A 3280 TYR cc_start: 0.8163 (t80) cc_final: 0.7879 (t80) REVERT: A 3450 MET cc_start: 0.7385 (ttt) cc_final: 0.7179 (ttt) REVERT: A 3535 ILE cc_start: 0.7545 (mt) cc_final: 0.7241 (mt) REVERT: A 3808 ASN cc_start: 0.8091 (t0) cc_final: 0.7694 (p0) REVERT: B 163 HIS cc_start: 0.6835 (m90) cc_final: 0.6455 (m90) REVERT: C 84 MET cc_start: 0.7336 (mpp) cc_final: 0.6782 (mpp) REVERT: C 115 MET cc_start: 0.7114 (tpt) cc_final: 0.6879 (tpt) REVERT: C 267 ILE cc_start: 0.8077 (pt) cc_final: 0.7850 (pt) REVERT: C 427 MET cc_start: 0.7975 (tmm) cc_final: 0.7658 (tmm) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2096 time to fit residues: 183.4781 Evaluate side-chains 386 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 352 optimal weight: 0.9980 chunk 415 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 56 optimal weight: 0.8980 chunk 431 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 ASN A2163 HIS ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN A2365 ASN A3113 ASN A3123 GLN A3251 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS B 515 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.128304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109463 restraints weight = 110566.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108943 restraints weight = 129657.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109952 restraints weight = 118522.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.110117 restraints weight = 80052.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110444 restraints weight = 77371.456| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39161 Z= 0.126 Angle : 0.665 12.848 53235 Z= 0.343 Chirality : 0.042 0.187 6062 Planarity : 0.005 0.086 6507 Dihedral : 13.623 63.439 5750 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.21 % Rotamer: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.12), residues: 4570 helix: -0.54 (0.10), residues: 2547 sheet: -1.28 (0.36), residues: 200 loop : -3.45 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1936 TYR 0.018 0.001 TYR A1940 PHE 0.040 0.001 PHE C 491 TRP 0.017 0.001 TRP A1207 HIS 0.015 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (39161) covalent geometry : angle 0.66543 / 0.34 (53235) hydrogen bonds : bond 0.03736 / 2.43 ( 1763) hydrogen bonds : angle 4.70731 / 3.30 ( 5067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 518 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8033 (tpt) cc_final: 0.7005 (tpp) REVERT: A 441 MET cc_start: 0.5948 (tpt) cc_final: 0.5586 (tpt) REVERT: A 994 TRP cc_start: 0.5189 (t-100) cc_final: 0.4340 (m-10) REVERT: A 1124 ILE cc_start: 0.8079 (pt) cc_final: 0.7581 (pt) REVERT: A 1127 CYS cc_start: 0.7541 (p) cc_final: 0.7153 (m) REVERT: A 1213 LYS cc_start: 0.8589 (pptt) cc_final: 0.7881 (mttt) REVERT: A 1583 MET cc_start: 0.8440 (tmm) cc_final: 0.8023 (tmm) REVERT: A 1739 TYR cc_start: 0.6889 (t80) cc_final: 0.6229 (t80) REVERT: A 1743 MET cc_start: 0.7890 (mmp) cc_final: 0.7520 (mmm) REVERT: A 1949 ILE cc_start: 0.8623 (mm) cc_final: 0.8212 (mt) REVERT: A 1986 ARG cc_start: 0.6876 (ptt-90) cc_final: 0.6626 (ptt90) REVERT: A 2002 LYS cc_start: 0.8056 (mppt) cc_final: 0.7526 (mppt) REVERT: A 2274 ILE cc_start: 0.7544 (pt) cc_final: 0.7271 (pt) REVERT: A 2281 MET cc_start: 0.7013 (tpt) cc_final: 0.6573 (tpt) REVERT: A 2877 SER cc_start: 0.8419 (p) cc_final: 0.7944 (p) REVERT: A 3256 MET cc_start: 0.7896 (tpp) cc_final: 0.7535 (tpt) REVERT: A 3280 TYR cc_start: 0.8205 (t80) cc_final: 0.7896 (t80) REVERT: A 3527 GLN cc_start: 0.7688 (tp40) cc_final: 0.7019 (tm-30) REVERT: A 3535 ILE cc_start: 0.7345 (mt) cc_final: 0.7109 (mt) REVERT: A 3808 ASN cc_start: 0.8062 (t0) cc_final: 0.7664 (p0) REVERT: B 163 HIS cc_start: 0.6729 (m90) cc_final: 0.6402 (m90) REVERT: C 84 MET cc_start: 0.7367 (mpp) cc_final: 0.6924 (mpp) REVERT: C 280 ASP cc_start: 0.4759 (p0) cc_final: 0.3760 (t70) REVERT: C 427 MET cc_start: 0.7936 (tmm) cc_final: 0.7650 (tmm) outliers start: 1 outliers final: 0 residues processed: 519 average time/residue: 0.2102 time to fit residues: 184.1459 Evaluate side-chains 395 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 424 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 409 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS A 998 ASN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS A2177 ASN A2270 ASN A2306 ASN A2365 ASN A3251 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108593 restraints weight = 110920.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107955 restraints weight = 148103.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108930 restraints weight = 136885.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109009 restraints weight = 90500.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109850 restraints weight = 83563.913| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39161 Z= 0.159 Angle : 0.701 13.217 53235 Z= 0.360 Chirality : 0.044 0.240 6062 Planarity : 0.005 0.077 6507 Dihedral : 13.613 63.891 5750 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.19 % Favored : 87.72 % Rotamer: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.12), residues: 4570 helix: -0.52 (0.10), residues: 2564 sheet: -1.23 (0.36), residues: 200 loop : -3.44 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1936 TYR 0.020 0.002 TYR B 530 PHE 0.041 0.002 PHE C 491 TRP 0.026 0.001 TRP A1207 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (39161) covalent geometry : angle 0.70094 / 0.36 (53235) hydrogen bonds : bond 0.03964 / 2.59 ( 1763) hydrogen bonds : angle 4.78567 / 3.36 ( 5067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8029 (tpt) cc_final: 0.6973 (tpp) REVERT: A 441 MET cc_start: 0.5919 (tpt) cc_final: 0.5595 (tpt) REVERT: A 765 LEU cc_start: 0.8534 (pt) cc_final: 0.8238 (pp) REVERT: A 1124 ILE cc_start: 0.8167 (pt) cc_final: 0.7635 (pt) REVERT: A 1127 CYS cc_start: 0.7625 (p) cc_final: 0.7180 (m) REVERT: A 1213 LYS cc_start: 0.8619 (pptt) cc_final: 0.7936 (mttt) REVERT: A 1392 MET cc_start: 0.8193 (mmm) cc_final: 0.7342 (mpp) REVERT: A 1583 MET cc_start: 0.8485 (tmm) cc_final: 0.8133 (tmm) REVERT: A 1739 TYR cc_start: 0.7081 (t80) cc_final: 0.6706 (t80) REVERT: A 1949 ILE cc_start: 0.8687 (mm) cc_final: 0.8408 (mm) REVERT: A 2002 LYS cc_start: 0.8058 (mppt) cc_final: 0.7520 (mppt) REVERT: A 2274 ILE cc_start: 0.7631 (pt) cc_final: 0.7336 (pt) REVERT: A 2279 ILE cc_start: 0.8583 (tt) cc_final: 0.8265 (mt) REVERT: A 2281 MET cc_start: 0.7032 (tpt) cc_final: 0.6604 (tpt) REVERT: A 3256 MET cc_start: 0.7953 (tpp) cc_final: 0.7630 (tpt) REVERT: A 3260 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6740 (tppt) REVERT: A 3280 TYR cc_start: 0.8150 (t80) cc_final: 0.7807 (t80) REVERT: A 3535 ILE cc_start: 0.7474 (mt) cc_final: 0.7216 (mt) REVERT: A 3808 ASN cc_start: 0.7980 (t0) cc_final: 0.7675 (p0) REVERT: B 62 MET cc_start: 0.8494 (ttm) cc_final: 0.8258 (tpp) REVERT: B 163 HIS cc_start: 0.6793 (m90) cc_final: 0.6428 (m90) REVERT: C 280 ASP cc_start: 0.4864 (p0) cc_final: 0.3904 (t0) REVERT: C 427 MET cc_start: 0.8013 (tmm) cc_final: 0.7635 (tmm) outliers start: 2 outliers final: 0 residues processed: 512 average time/residue: 0.2153 time to fit residues: 187.8439 Evaluate side-chains 390 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 298 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.0870 chunk 159 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS A1394 HIS ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 ASN ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS A2365 ASN A3113 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.128304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109586 restraints weight = 110359.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108631 restraints weight = 141318.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109539 restraints weight = 124802.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109890 restraints weight = 87556.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.110041 restraints weight = 82387.845| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 39161 Z= 0.135 Angle : 0.689 13.538 53235 Z= 0.352 Chirality : 0.043 0.223 6062 Planarity : 0.005 0.080 6507 Dihedral : 13.545 63.222 5750 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.33 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 4570 helix: -0.39 (0.10), residues: 2556 sheet: -1.20 (0.37), residues: 197 loop : -3.34 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 891 TYR 0.019 0.001 TYR B 400 PHE 0.039 0.002 PHE C 491 TRP 0.031 0.001 TRP A2125 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (39161) covalent geometry : angle 0.68895 / 0.35 (53235) hydrogen bonds : bond 0.03740 / 2.43 ( 1763) hydrogen bonds : angle 4.67370 / 3.28 ( 5067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.7992 (tpt) cc_final: 0.6969 (tpp) REVERT: A 441 MET cc_start: 0.5822 (tpt) cc_final: 0.5519 (tpt) REVERT: A 994 TRP cc_start: 0.4172 (t-100) cc_final: 0.3610 (m-10) REVERT: A 1124 ILE cc_start: 0.8106 (pt) cc_final: 0.7583 (pt) REVERT: A 1127 CYS cc_start: 0.7669 (p) cc_final: 0.7196 (m) REVERT: A 1213 LYS cc_start: 0.8624 (pptt) cc_final: 0.7910 (mttt) REVERT: A 1369 MET cc_start: 0.6055 (mpp) cc_final: 0.5810 (mpp) REVERT: A 1583 MET cc_start: 0.8411 (tmm) cc_final: 0.8063 (tmm) REVERT: A 1949 ILE cc_start: 0.8695 (mm) cc_final: 0.8421 (mm) REVERT: A 2002 LYS cc_start: 0.8055 (mppt) cc_final: 0.7497 (mppt) REVERT: A 2104 MET cc_start: 0.6636 (tmm) cc_final: 0.6097 (tmm) REVERT: A 2274 ILE cc_start: 0.7590 (pt) cc_final: 0.7347 (pt) REVERT: A 2279 ILE cc_start: 0.8581 (tt) cc_final: 0.8310 (mt) REVERT: A 2281 MET cc_start: 0.6952 (tpt) cc_final: 0.6523 (tpt) REVERT: A 3256 MET cc_start: 0.8009 (tpp) cc_final: 0.7667 (tpt) REVERT: A 3260 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6774 (tppt) REVERT: A 3280 TYR cc_start: 0.8152 (t80) cc_final: 0.7810 (t80) REVERT: A 3527 GLN cc_start: 0.7690 (tp40) cc_final: 0.7047 (tm-30) REVERT: A 3808 ASN cc_start: 0.7930 (t0) cc_final: 0.7620 (p0) REVERT: B 163 HIS cc_start: 0.6726 (m90) cc_final: 0.6429 (m90) REVERT: B 334 THR cc_start: 0.7226 (m) cc_final: 0.6797 (m) REVERT: C 84 MET cc_start: 0.7474 (mpp) cc_final: 0.6959 (mpp) REVERT: C 267 ILE cc_start: 0.8143 (pt) cc_final: 0.7888 (pt) REVERT: C 280 ASP cc_start: 0.4723 (p0) cc_final: 0.3771 (t70) REVERT: C 427 MET cc_start: 0.8018 (tmm) cc_final: 0.7804 (tmm) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.2069 time to fit residues: 187.0350 Evaluate side-chains 400 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 185 optimal weight: 7.9990 chunk 341 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 368 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 223 optimal weight: 0.0980 chunk 373 optimal weight: 10.0000 chunk 202 optimal weight: 0.0870 chunk 464 optimal weight: 40.0000 chunk 218 optimal weight: 1.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 533 HIS A 998 ASN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS A2306 ASN A2365 ASN A3113 ASN A3122 HIS ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS B 515 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109959 restraints weight = 110127.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109084 restraints weight = 120995.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.109923 restraints weight = 111706.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110390 restraints weight = 77318.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110512 restraints weight = 73220.208| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39161 Z= 0.124 Angle : 0.679 13.685 53235 Z= 0.345 Chirality : 0.043 0.286 6062 Planarity : 0.005 0.081 6507 Dihedral : 13.459 61.781 5750 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.03 % Favored : 88.88 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.12), residues: 4570 helix: -0.28 (0.10), residues: 2553 sheet: -1.02 (0.37), residues: 200 loop : -3.30 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1936 TYR 0.028 0.001 TYR A2312 PHE 0.040 0.001 PHE A 707 TRP 0.030 0.001 TRP A1207 HIS 0.015 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (39161) covalent geometry : angle 0.67868 / 0.35 (53235) hydrogen bonds : bond 0.03572 / 2.32 ( 1763) hydrogen bonds : angle 4.59551 / 3.22 ( 5067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.7975 (tpt) cc_final: 0.6961 (tpp) REVERT: A 441 MET cc_start: 0.5735 (tpt) cc_final: 0.5508 (tpt) REVERT: A 1124 ILE cc_start: 0.8125 (pt) cc_final: 0.7755 (pt) REVERT: A 1127 CYS cc_start: 0.7658 (p) cc_final: 0.6580 (t) REVERT: A 1213 LYS cc_start: 0.8669 (pptt) cc_final: 0.7937 (mttt) REVERT: A 1369 MET cc_start: 0.6070 (mpp) cc_final: 0.5835 (mpp) REVERT: A 1583 MET cc_start: 0.8393 (tmm) cc_final: 0.8055 (tmm) REVERT: A 1788 ARG cc_start: 0.6012 (mtt-85) cc_final: 0.5227 (mtp180) REVERT: A 1949 ILE cc_start: 0.8690 (mm) cc_final: 0.8418 (mm) REVERT: A 2002 LYS cc_start: 0.7932 (mppt) cc_final: 0.7416 (mppt) REVERT: A 2274 ILE cc_start: 0.7527 (pt) cc_final: 0.7304 (pt) REVERT: A 2279 ILE cc_start: 0.8592 (tt) cc_final: 0.8339 (mt) REVERT: A 2281 MET cc_start: 0.6966 (tpt) cc_final: 0.6516 (tpt) REVERT: A 3111 MET cc_start: 0.8065 (ttm) cc_final: 0.7670 (tpp) REVERT: A 3280 TYR cc_start: 0.8205 (t80) cc_final: 0.7882 (t80) REVERT: A 3527 GLN cc_start: 0.7617 (tp40) cc_final: 0.6949 (tm-30) REVERT: A 3933 GLU cc_start: 0.8191 (tt0) cc_final: 0.7851 (tt0) REVERT: B 163 HIS cc_start: 0.6679 (m90) cc_final: 0.6424 (m90) REVERT: B 334 THR cc_start: 0.7023 (m) cc_final: 0.6799 (m) REVERT: C 84 MET cc_start: 0.7466 (mpp) cc_final: 0.6989 (mpp) REVERT: C 267 ILE cc_start: 0.8163 (pt) cc_final: 0.7914 (pt) REVERT: C 280 ASP cc_start: 0.4596 (p0) cc_final: 0.3792 (t0) REVERT: C 427 MET cc_start: 0.7988 (tmm) cc_final: 0.7744 (tmm) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.2064 time to fit residues: 187.4641 Evaluate side-chains 410 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 258 optimal weight: 4.9990 chunk 299 optimal weight: 0.0370 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 327 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 246 optimal weight: 0.0970 chunk 16 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 overall best weight: 0.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS A1394 HIS ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2163 HIS A2365 ASN A3113 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN A3808 ASN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.111447 restraints weight = 109455.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.110633 restraints weight = 125938.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111499 restraints weight = 104538.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111760 restraints weight = 76348.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111863 restraints weight = 71507.456| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39161 Z= 0.124 Angle : 0.681 13.497 53235 Z= 0.344 Chirality : 0.043 0.222 6062 Planarity : 0.005 0.081 6507 Dihedral : 13.356 60.548 5750 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.11 % Favored : 89.80 % Rotamer: Outliers : 0.02 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4570 helix: -0.15 (0.10), residues: 2553 sheet: -0.86 (0.37), residues: 194 loop : -3.24 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1936 TYR 0.029 0.001 TYR A4039 PHE 0.035 0.001 PHE C 491 TRP 0.090 0.002 TRP A4027 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (39161) covalent geometry : angle 0.68122 / 0.34 (53235) hydrogen bonds : bond 0.03338 / 2.17 ( 1763) hydrogen bonds : angle 4.45551 / 3.12 ( 5067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 546 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8026 (tpt) cc_final: 0.6841 (tpp) REVERT: A 441 MET cc_start: 0.5794 (tpt) cc_final: 0.5561 (tpt) REVERT: A 468 LEU cc_start: 0.8332 (pp) cc_final: 0.7867 (tp) REVERT: A 1124 ILE cc_start: 0.8125 (pt) cc_final: 0.7779 (pt) REVERT: A 1127 CYS cc_start: 0.7743 (p) cc_final: 0.6655 (t) REVERT: A 1213 LYS cc_start: 0.8634 (pptt) cc_final: 0.7937 (mttt) REVERT: A 1369 MET cc_start: 0.5982 (mpp) cc_final: 0.5714 (mpp) REVERT: A 1583 MET cc_start: 0.8310 (tmm) cc_final: 0.7975 (tmm) REVERT: A 1788 ARG cc_start: 0.5869 (mtt-85) cc_final: 0.5165 (mtp180) REVERT: A 1949 ILE cc_start: 0.8624 (mm) cc_final: 0.8324 (mm) REVERT: A 2002 LYS cc_start: 0.7920 (mppt) cc_final: 0.7346 (mppt) REVERT: A 2085 MET cc_start: 0.2594 (tpp) cc_final: 0.2040 (tmm) REVERT: A 2274 ILE cc_start: 0.7437 (pt) cc_final: 0.7156 (pt) REVERT: A 2279 ILE cc_start: 0.8502 (tt) cc_final: 0.8220 (mt) REVERT: A 2281 MET cc_start: 0.6974 (tpt) cc_final: 0.6553 (tpt) REVERT: A 2478 MET cc_start: 0.7480 (ttp) cc_final: 0.7055 (ttm) REVERT: A 3111 MET cc_start: 0.7849 (ttm) cc_final: 0.7498 (tpp) REVERT: A 3256 MET cc_start: 0.8031 (tpp) cc_final: 0.7642 (tpt) REVERT: A 3280 TYR cc_start: 0.8273 (t80) cc_final: 0.7980 (t80) REVERT: A 3527 GLN cc_start: 0.7292 (tp40) cc_final: 0.6776 (tm-30) REVERT: B 334 THR cc_start: 0.6996 (m) cc_final: 0.6580 (m) REVERT: B 516 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8157 (pptt) REVERT: C 84 MET cc_start: 0.7526 (mpp) cc_final: 0.7018 (mpp) REVERT: C 267 ILE cc_start: 0.8063 (pt) cc_final: 0.7837 (pt) REVERT: C 280 ASP cc_start: 0.4701 (p0) cc_final: 0.4100 (t70) outliers start: 1 outliers final: 0 residues processed: 547 average time/residue: 0.2218 time to fit residues: 206.8622 Evaluate side-chains 416 residues out of total 4142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 365 optimal weight: 10.0000 chunk 338 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 chunk 453 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 457 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 533 HIS A 998 ASN A1367 HIS ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 HIS A2163 HIS A2306 ASN A2365 ASN A3113 ASN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3634 GLN ** A3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111785 restraints weight = 109912.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111000 restraints weight = 134372.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111717 restraints weight = 121625.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.112090 restraints weight = 84447.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112267 restraints weight = 79764.470| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39161 Z= 0.123 Angle : 0.678 13.415 53235 Z= 0.341 Chirality : 0.042 0.271 6062 Planarity : 0.005 0.082 6507 Dihedral : 13.324 59.962 5750 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.46 % Favored : 89.47 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.94 (0.12), residues: 4570 helix: -0.05 (0.11), residues: 2542 sheet: -0.82 (0.37), residues: 194 loop : -3.21 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 675 TYR 0.023 0.001 TYR A4039 PHE 0.024 0.001 PHE A3571 TRP 0.052 0.002 TRP A4027 HIS 0.014 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (39161) covalent geometry : angle 0.67774 / 0.34 (53235) hydrogen bonds : bond 0.03353 / 2.19 ( 1763) hydrogen bonds : angle 4.44961 / 3.12 ( 5067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.93 seconds wall clock time: 99 minutes 12.50 seconds (5952.50 seconds total)