Starting phenix.real_space_refine on Tue May 5 11:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552.map" model { file = "/net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pe3_71552/05_2026/9pe3_71552_trim.cif" } resolution = 3.26 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= 0.003 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 70 5.16 5 C 9243 2.51 5 N 2197 2.21 5 O 2405 1.98 5 H 12582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1595, 24710 Classifications: {'peptide': 1595} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1526} Chain breaks: 8 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 5, 'GLU:plan': 16, 'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 4, 'ARG:plan': 13, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 272 Chain: "G" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 857 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 7, 'TRANS': 56} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 872 Unusual residues: {'3PE': 1, 'NAG': 1, 'UDP': 1, 'Y01': 22} Classifications: {'undetermined': 25, 'water': 3} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.75, per 1000 atoms: 0.18 Number of scatterers: 26500 At special positions: 0 Unit cell: (94.92, 118.44, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 3 15.00 O 2405 8.00 N 2197 7.00 C 9243 6.00 H 12582 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A1849 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 818.0 milliseconds 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3134 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 3 sheets defined 68.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.788A pdb=" N LEU A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 4.018A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.554A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.512A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 338 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.595A pdb=" N GLN A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.907A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 removed outlier: 3.744A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.722A pdb=" N VAL A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 4.326A pdb=" N TRP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 463 " --> pdb=" O HIS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 518 removed outlier: 4.337A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 removed outlier: 3.979A pdb=" N ARG A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 557 through 583 removed outlier: 4.245A pdb=" N HIS A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 640 removed outlier: 3.793A pdb=" N TRP A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.569A pdb=" N ARG A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 711 removed outlier: 3.585A pdb=" N LYS A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Proline residue: A 673 - end of helix removed outlier: 4.255A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 736 through 741 removed outlier: 4.155A pdb=" N MET A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 741' Processing helix chain 'A' and resid 745 through 764 removed outlier: 3.959A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 3.919A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 775 " --> pdb=" O HIS A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 813 through 828 removed outlier: 3.667A pdb=" N SER A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 868 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 949 through 972 removed outlier: 3.597A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.733A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.859A pdb=" N LEU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1081 through 1091 removed outlier: 4.366A pdb=" N ASN A1085 " --> pdb=" O GLY A1081 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A1091 " --> pdb=" O ASN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1114 removed outlier: 3.822A pdb=" N LYS A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1121 Processing helix chain 'A' and resid 1163 through 1188 removed outlier: 4.670A pdb=" N GLY A1171 " --> pdb=" O ASP A1167 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A1172 " --> pdb=" O VAL A1168 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A1173 " --> pdb=" O ALA A1169 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A1180 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A1186 " --> pdb=" O ARG A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1251 through 1271 removed outlier: 4.041A pdb=" N LEU A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1282 removed outlier: 3.582A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1294 through 1325 removed outlier: 4.592A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1313 " --> pdb=" O GLN A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1353 through 1369 removed outlier: 3.591A pdb=" N ARG A1357 " --> pdb=" O ASP A1353 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1369 " --> pdb=" O VAL A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1382 through 1397 Processing helix chain 'A' and resid 1397 through 1419 removed outlier: 3.617A pdb=" N PHE A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1403 " --> pdb=" O PRO A1399 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1404 " --> pdb=" O MET A1400 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1418 " --> pdb=" O LEU A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1447 removed outlier: 4.278A pdb=" N GLY A1447 " --> pdb=" O SER A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1467 Processing helix chain 'A' and resid 1471 through 1490 removed outlier: 4.101A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) Proline residue: A1486 - end of helix Processing helix chain 'A' and resid 1495 through 1512 Processing helix chain 'A' and resid 1521 through 1532 removed outlier: 3.634A pdb=" N ARG A1527 " --> pdb=" O ILE A1523 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A1528 " --> pdb=" O GLY A1524 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A1529 " --> pdb=" O TYR A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1584 Proline residue: A1567 - end of helix Processing helix chain 'A' and resid 1591 through 1595 removed outlier: 3.574A pdb=" N ARG A1595 " --> pdb=" O ASP A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1625 removed outlier: 3.546A pdb=" N ILE A1602 " --> pdb=" O SER A1598 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1608 " --> pdb=" O ILE A1604 " (cutoff:3.500A) Proline residue: A1609 - end of helix Processing helix chain 'A' and resid 1638 through 1665 removed outlier: 4.361A pdb=" N MET A1642 " --> pdb=" O THR A1638 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A1643 " --> pdb=" O GLY A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1695 removed outlier: 3.773A pdb=" N LEU A1673 " --> pdb=" O PHE A1669 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1754 removed outlier: 3.622A pdb=" N SER A1738 " --> pdb=" O VAL A1734 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1760 removed outlier: 3.706A pdb=" N ILE A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1773 removed outlier: 3.816A pdb=" N PHE A1766 " --> pdb=" O LYS A1762 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1825 removed outlier: 3.680A pdb=" N LEU A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) Proline residue: A1818 - end of helix removed outlier: 4.102A pdb=" N ALA A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A1824 " --> pdb=" O VAL A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1857 removed outlier: 4.184A pdb=" N THR A1857 " --> pdb=" O SER A1853 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 118 removed outlier: 3.744A pdb=" N THR G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 125 removed outlier: 4.334A pdb=" N ALA G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 781 Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1072 removed outlier: 3.883A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A1047 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A1151 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG A1235 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A1150 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A1154 " --> pdb=" O CYS A1239 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR A1241 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 10.973A pdb=" N TYR A1156 " --> pdb=" O TYR A1241 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLN A1243 " --> pdb=" O TYR A1156 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N PHE A1158 " --> pdb=" O GLN A1243 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N GLY A1245 " --> pdb=" O PHE A1158 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12551 1.03 - 1.23: 103 1.23 - 1.42: 5805 1.42 - 1.62: 8332 1.62 - 1.81: 118 Bond restraints: 26909 Sorted by residual: bond pdb=" C4' UDP A2025 " pdb=" C3' UDP A2025 " ideal model delta sigma weight residual 1.526 1.340 0.186 1.30e-02 5.92e+03 2.05e+02 bond pdb=" C4' UDP A2025 " pdb=" O4' UDP A2025 " ideal model delta sigma weight residual 1.444 1.612 -0.168 1.30e-02 5.92e+03 1.67e+02 bond pdb=" C5 UDP A2025 " pdb=" H5 UDP A2025 " ideal model delta sigma weight residual 0.930 1.085 -0.155 1.40e-02 5.10e+03 1.23e+02 bond pdb=" C6 UDP A2025 " pdb=" H6 UDP A2025 " ideal model delta sigma weight residual 0.930 1.083 -0.153 1.40e-02 5.10e+03 1.19e+02 bond pdb=" C1' UDP A2025 " pdb=" H1' UDP A2025 " ideal model delta sigma weight residual 0.970 1.086 -0.116 1.10e-02 8.26e+03 1.11e+02 ... (remaining 26904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.17: 48067 9.17 - 18.35: 49 18.35 - 27.52: 0 27.52 - 36.70: 1 36.70 - 45.87: 2 Bond angle restraints: 48119 Sorted by residual: angle pdb="HD21 ASN A1849 " pdb=" ND2 ASN A1849 " pdb="HD22 ASN A1849 " ideal model delta sigma weight residual 120.00 74.13 45.87 3.00e+00 1.11e-01 2.34e+02 angle pdb=" CG ASN A1849 " pdb=" ND2 ASN A1849 " pdb="HD22 ASN A1849 " ideal model delta sigma weight residual 120.00 76.16 43.84 3.00e+00 1.11e-01 2.14e+02 angle pdb=" CG ASN A1849 " pdb=" ND2 ASN A1849 " pdb="HD21 ASN A1849 " ideal model delta sigma weight residual 120.00 150.29 -30.29 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C2 UDP A2025 " pdb=" N3 UDP A2025 " pdb=" C4 UDP A2025 " ideal model delta sigma weight residual 126.93 120.17 6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" O2B UDP A2025 " pdb=" PB UDP A2025 " pdb=" O3A UDP A2025 " ideal model delta sigma weight residual 102.95 109.14 -6.19 1.00e+00 1.00e+00 3.83e+01 ... (remaining 48114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 13313 24.88 - 49.75: 574 49.75 - 74.63: 195 74.63 - 99.51: 13 99.51 - 124.38: 12 Dihedral angle restraints: 14107 sinusoidal: 8125 harmonic: 5982 Sorted by residual: dihedral pdb=" CAZ Y01 A2013 " pdb=" CAV Y01 A2013 " pdb=" CBC Y01 A2013 " pdb=" OAW Y01 A2013 " ideal model delta sinusoidal sigma weight residual -174.31 -49.93 -124.38 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAR Y01 A2013 " pdb=" CAV Y01 A2013 " pdb=" CBC Y01 A2013 " pdb=" CAZ Y01 A2013 " ideal model delta sinusoidal sigma weight residual 55.40 -67.95 123.35 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CAR Y01 A2012 " pdb=" CAV Y01 A2012 " pdb=" CBC Y01 A2012 " pdb=" CAZ Y01 A2012 " ideal model delta sinusoidal sigma weight residual 55.40 -54.06 109.46 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 14104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2028 0.092 - 0.184: 119 0.184 - 0.276: 27 0.276 - 0.368: 38 0.368 - 0.461: 29 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CBH Y01 A2013 " pdb=" CAT Y01 A2013 " pdb=" CAZ Y01 A2013 " pdb=" CBF Y01 A2013 " both_signs ideal model delta sigma weight residual False -2.85 -3.31 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CBH Y01 A2012 " pdb=" CAT Y01 A2012 " pdb=" CAZ Y01 A2012 " pdb=" CBF Y01 A2012 " both_signs ideal model delta sigma weight residual False -2.85 -3.31 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CBH Y01 A2014 " pdb=" CAT Y01 A2014 " pdb=" CAZ Y01 A2014 " pdb=" CBF Y01 A2014 " both_signs ideal model delta sigma weight residual False -2.85 -3.29 0.43 2.00e-01 2.50e+01 4.67e+00 ... (remaining 2238 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 475 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C TYR A 475 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 475 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 476 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 474 " -0.009 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" N TYR A 475 " 0.027 2.00e-02 2.50e+03 pdb=" CA TYR A 475 " -0.007 2.00e-02 2.50e+03 pdb=" H TYR A 475 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 474 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C PHE A 474 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 474 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 475 " 0.009 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1270 2.20 - 2.80: 51930 2.80 - 3.40: 73714 3.40 - 4.00: 93604 4.00 - 4.60: 146486 Nonbonded interactions: 367004 Sorted by model distance: nonbonded pdb=" O SER A 603 " pdb=" HG1 THR A 607 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP A1102 " pdb=" H ALA A1103 " model vdw 1.628 2.450 nonbonded pdb=" O ALA A1201 " pdb=" HG1 THR A1205 " model vdw 1.628 2.450 nonbonded pdb=" O THR A 218 " pdb="HH22 ARG A1207 " model vdw 1.652 2.450 nonbonded pdb=" HG SER A1307 " pdb=" OH TYR A1358 " model vdw 1.655 2.450 ... (remaining 366999 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.007 0.186 14334 Z= 0.411 Angle : 1.121 14.812 19623 Z= 0.433 Chirality : 0.079 0.461 2241 Planarity : 0.003 0.036 2350 Dihedral : 15.258 124.385 6431 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.38 % Allowed : 4.78 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.44 (0.21), residues: 1639 helix: 2.63 (0.16), residues: 1003 sheet: 1.84 (0.63), residues: 58 loop : -0.26 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1273 TYR 0.009 0.001 TYR A1409 PHE 0.017 0.001 PHE A1669 TRP 0.010 0.001 TRP A 289 HIS 0.003 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00737 (14327) covalent geometry : angle 1.11441 (19604) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.58837 ( 4) hydrogen bonds : bond 0.12758 ( 768) hydrogen bonds : angle 5.18413 ( 2271) link_ALPHA1-3 : bond 0.00093 ( 1) link_ALPHA1-3 : angle 3.62648 ( 3) link_ALPHA1-6 : bond 0.00564 ( 1) link_ALPHA1-6 : angle 1.76899 ( 3) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 1.81464 ( 6) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 8.59469 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 240 time to evaluate : 0.664 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 182 MET cc_start: 0.8104 (ttp) cc_final: 0.7765 (tmm) REVERT: A 283 GLU cc_start: 0.7644 (pt0) cc_final: 0.7389 (mt-10) REVERT: A 293 MET cc_start: 0.8583 (mmt) cc_final: 0.8361 (mmt) REVERT: A 583 MET cc_start: 0.8876 (mmp) cc_final: 0.8665 (mmm) REVERT: A 780 VAL cc_start: 0.7270 (m) cc_final: 0.6974 (m) REVERT: A 1088 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (t70) REVERT: A 1130 VAL cc_start: 0.9464 (t) cc_final: 0.9043 (m) REVERT: A 1266 MET cc_start: 0.8345 (mmm) cc_final: 0.8036 (mmm) REVERT: A 1400 MET cc_start: 0.8410 (mtm) cc_final: 0.8027 (mtp) REVERT: A 1440 ILE cc_start: 0.8914 (mt) cc_final: 0.8696 (tp) REVERT: A 1442 TYR cc_start: 0.8534 (t80) cc_final: 0.8080 (t80) REVERT: A 1503 TYR cc_start: 0.7909 (t80) cc_final: 0.7532 (t80) REVERT: A 1562 MET cc_start: 0.5423 (mmt) cc_final: 0.5058 (tmm) REVERT: A 1672 MET cc_start: 0.8539 (ttp) cc_final: 0.8150 (tmm) REVERT: A 1733 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8003 (mttt) REVERT: A 1793 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7719 (mtm180) REVERT: A 1796 MET cc_start: 0.8333 (ttm) cc_final: 0.8114 (ttm) outliers start: 5 outliers final: 3 residues processed: 245 average time/residue: 0.2758 time to fit residues: 96.3437 Evaluate side-chains 155 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1133 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN A1583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081571 restraints weight = 72490.045| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.35 r_work: 0.2933 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14334 Z= 0.198 Angle : 0.595 15.204 19623 Z= 0.297 Chirality : 0.039 0.295 2241 Planarity : 0.004 0.060 2350 Dihedral : 12.494 107.190 3578 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.21 % Allowed : 8.80 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.31 (0.21), residues: 1639 helix: 2.52 (0.16), residues: 1019 sheet: 1.35 (0.64), residues: 58 loop : -0.32 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 376 TYR 0.012 0.001 TYR A 475 PHE 0.015 0.001 PHE A1203 TRP 0.010 0.001 TRP A 289 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00434 (14327) covalent geometry : angle 0.58098 (19604) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.86810 ( 4) hydrogen bonds : bond 0.05474 ( 768) hydrogen bonds : angle 4.60705 ( 2271) link_ALPHA1-3 : bond 0.00510 ( 1) link_ALPHA1-3 : angle 4.55058 ( 3) link_ALPHA1-6 : bond 0.00612 ( 1) link_ALPHA1-6 : angle 2.11635 ( 3) link_BETA1-4 : bond 0.00658 ( 2) link_BETA1-4 : angle 1.62430 ( 6) link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 8.88790 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.684 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 182 MET cc_start: 0.8365 (ttp) cc_final: 0.7950 (tmm) REVERT: A 283 GLU cc_start: 0.7818 (pt0) cc_final: 0.7519 (mt-10) REVERT: A 293 MET cc_start: 0.8620 (mmt) cc_final: 0.8389 (mmt) REVERT: A 474 PHE cc_start: 0.9276 (m-10) cc_final: 0.8927 (m-80) REVERT: A 475 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: A 583 MET cc_start: 0.8901 (mmp) cc_final: 0.8680 (mmm) REVERT: A 659 THR cc_start: 0.8777 (m) cc_final: 0.8525 (p) REVERT: A 984 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8710 (mm-30) REVERT: A 1266 MET cc_start: 0.8503 (mmm) cc_final: 0.8110 (mmm) REVERT: A 1294 HIS cc_start: 0.8225 (m-70) cc_final: 0.7925 (m-70) REVERT: A 1377 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7338 (tp30) REVERT: A 1400 MET cc_start: 0.8402 (mtm) cc_final: 0.8021 (mtp) REVERT: A 1503 TYR cc_start: 0.8086 (t80) cc_final: 0.7735 (t80) REVERT: A 1672 MET cc_start: 0.8614 (ttp) cc_final: 0.8192 (tmm) REVERT: A 1733 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8026 (mttt) REVERT: A 1793 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7672 (mtm180) REVERT: A 1814 CYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (t) outliers start: 16 outliers final: 13 residues processed: 172 average time/residue: 0.2869 time to fit residues: 71.8016 Evaluate side-chains 157 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1797 VAL Chi-restraints excluded: chain A residue 1814 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077743 restraints weight = 72797.143| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.37 r_work: 0.2922 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14334 Z= 0.159 Angle : 0.528 15.563 19623 Z= 0.267 Chirality : 0.037 0.276 2241 Planarity : 0.004 0.049 2350 Dihedral : 11.311 91.391 3578 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 9.56 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.32 (0.21), residues: 1639 helix: 2.56 (0.16), residues: 1016 sheet: 0.82 (0.66), residues: 60 loop : -0.30 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1444 TYR 0.011 0.001 TYR A 968 PHE 0.019 0.001 PHE A1500 TRP 0.009 0.001 TRP A 289 HIS 0.004 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00349 (14327) covalent geometry : angle 0.51293 (19604) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.96745 ( 4) hydrogen bonds : bond 0.04990 ( 768) hydrogen bonds : angle 4.37073 ( 2271) link_ALPHA1-3 : bond 0.00523 ( 1) link_ALPHA1-3 : angle 3.84425 ( 3) link_ALPHA1-6 : bond 0.00780 ( 1) link_ALPHA1-6 : angle 2.18634 ( 3) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 1.51465 ( 6) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 9.06073 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.692 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 182 MET cc_start: 0.8346 (ttp) cc_final: 0.8072 (tmm) REVERT: A 283 GLU cc_start: 0.7803 (pt0) cc_final: 0.7526 (mt-10) REVERT: A 293 MET cc_start: 0.8576 (mmt) cc_final: 0.8348 (mmt) REVERT: A 474 PHE cc_start: 0.9295 (m-10) cc_final: 0.8912 (m-80) REVERT: A 583 MET cc_start: 0.8836 (mmp) cc_final: 0.8613 (mmm) REVERT: A 659 THR cc_start: 0.8825 (m) cc_final: 0.8586 (p) REVERT: A 935 TYR cc_start: 0.7648 (m-80) cc_final: 0.7439 (t80) REVERT: A 984 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8711 (mm-30) REVERT: A 1102 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: A 1195 HIS cc_start: 0.7318 (m-70) cc_final: 0.6748 (m-70) REVERT: A 1266 MET cc_start: 0.8464 (mmm) cc_final: 0.8067 (mmm) REVERT: A 1377 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7284 (tp30) REVERT: A 1391 PHE cc_start: 0.7025 (m-80) cc_final: 0.6741 (t80) REVERT: A 1400 MET cc_start: 0.8411 (mtm) cc_final: 0.8000 (mtp) REVERT: A 1503 TYR cc_start: 0.8042 (t80) cc_final: 0.7825 (t80) REVERT: A 1522 TRP cc_start: 0.8160 (t60) cc_final: 0.7564 (t60) REVERT: A 1672 MET cc_start: 0.8538 (ttp) cc_final: 0.8142 (tmm) REVERT: A 1733 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8086 (mttt) REVERT: A 1793 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7689 (mtm180) outliers start: 17 outliers final: 14 residues processed: 165 average time/residue: 0.2863 time to fit residues: 68.4944 Evaluate side-chains 156 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076366 restraints weight = 73318.688| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.34 r_work: 0.2897 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14334 Z= 0.204 Angle : 0.555 16.055 19623 Z= 0.280 Chirality : 0.038 0.313 2241 Planarity : 0.004 0.059 2350 Dihedral : 10.591 78.452 3578 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.29 % Allowed : 10.02 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.28 (0.21), residues: 1639 helix: 2.54 (0.16), residues: 1016 sheet: 0.78 (0.66), residues: 60 loop : -0.36 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1444 TYR 0.011 0.001 TYR A1292 PHE 0.015 0.001 PHE A1203 TRP 0.010 0.001 TRP A 289 HIS 0.005 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00455 (14327) covalent geometry : angle 0.53915 (19604) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.09736 ( 4) hydrogen bonds : bond 0.04949 ( 768) hydrogen bonds : angle 4.37651 ( 2271) link_ALPHA1-3 : bond 0.00528 ( 1) link_ALPHA1-3 : angle 4.12764 ( 3) link_ALPHA1-6 : bond 0.00832 ( 1) link_ALPHA1-6 : angle 2.25771 ( 3) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 1.60415 ( 6) link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 9.36930 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.886 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: A 283 GLU cc_start: 0.7829 (pt0) cc_final: 0.7563 (mt-10) REVERT: A 293 MET cc_start: 0.8564 (mmt) cc_final: 0.8337 (mmt) REVERT: A 474 PHE cc_start: 0.9298 (m-10) cc_final: 0.8873 (m-80) REVERT: A 475 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: A 583 MET cc_start: 0.8814 (mmp) cc_final: 0.8603 (mmm) REVERT: A 935 TYR cc_start: 0.7659 (m-80) cc_final: 0.7403 (t80) REVERT: A 984 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8726 (mm-30) REVERT: A 1377 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7282 (tp30) REVERT: A 1400 MET cc_start: 0.8438 (mtm) cc_final: 0.8008 (mtp) REVERT: A 1522 TRP cc_start: 0.8112 (t60) cc_final: 0.7566 (t60) REVERT: A 1672 MET cc_start: 0.8574 (ttp) cc_final: 0.8182 (tmm) REVERT: A 1733 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8070 (mttt) REVERT: A 1793 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7673 (mtm180) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.2894 time to fit residues: 67.2078 Evaluate side-chains 146 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080186 restraints weight = 72939.196| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.32 r_work: 0.2909 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14334 Z= 0.159 Angle : 0.527 15.872 19623 Z= 0.264 Chirality : 0.037 0.310 2241 Planarity : 0.004 0.054 2350 Dihedral : 9.806 68.449 3576 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.37 % Allowed : 10.32 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.34 (0.21), residues: 1639 helix: 2.59 (0.16), residues: 1015 sheet: 0.65 (0.66), residues: 60 loop : -0.31 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1444 TYR 0.009 0.001 TYR A1292 PHE 0.015 0.001 PHE A1203 TRP 0.009 0.001 TRP A 289 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00355 (14327) covalent geometry : angle 0.51096 (19604) SS BOND : bond 0.00461 ( 2) SS BOND : angle 0.87583 ( 4) hydrogen bonds : bond 0.04710 ( 768) hydrogen bonds : angle 4.24795 ( 2271) link_ALPHA1-3 : bond 0.00209 ( 1) link_ALPHA1-3 : angle 3.99524 ( 3) link_ALPHA1-6 : bond 0.01075 ( 1) link_ALPHA1-6 : angle 1.57960 ( 3) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 1.56475 ( 6) link_NAG-ASN : bond 0.00019 ( 1) link_NAG-ASN : angle 9.21809 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.707 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: A 283 GLU cc_start: 0.7862 (pt0) cc_final: 0.7595 (mt-10) REVERT: A 293 MET cc_start: 0.8620 (mmt) cc_final: 0.8382 (mmt) REVERT: A 475 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: A 583 MET cc_start: 0.8834 (mmp) cc_final: 0.8618 (mmm) REVERT: A 935 TYR cc_start: 0.7689 (m-80) cc_final: 0.7418 (t80) REVERT: A 1377 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7328 (tp30) REVERT: A 1391 PHE cc_start: 0.7023 (m-80) cc_final: 0.6697 (t80) REVERT: A 1400 MET cc_start: 0.8497 (mtm) cc_final: 0.8040 (mtp) REVERT: A 1522 TRP cc_start: 0.8050 (t60) cc_final: 0.7547 (t60) REVERT: A 1672 MET cc_start: 0.8546 (ttp) cc_final: 0.8193 (tmm) REVERT: A 1793 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7642 (mtm180) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.2762 time to fit residues: 61.7120 Evaluate side-chains 139 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.076456 restraints weight = 73191.665| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.37 r_work: 0.2904 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14334 Z= 0.158 Angle : 0.519 16.060 19623 Z= 0.259 Chirality : 0.036 0.251 2241 Planarity : 0.003 0.036 2350 Dihedral : 9.377 62.192 3576 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.52 % Allowed : 10.55 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.41 (0.21), residues: 1639 helix: 2.65 (0.16), residues: 1014 sheet: 0.53 (0.66), residues: 60 loop : -0.25 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 134 TYR 0.009 0.001 TYR A 308 PHE 0.014 0.001 PHE A1203 TRP 0.009 0.001 TRP A 289 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00352 (14327) covalent geometry : angle 0.50232 (19604) SS BOND : bond 0.00370 ( 2) SS BOND : angle 0.76911 ( 4) hydrogen bonds : bond 0.04589 ( 768) hydrogen bonds : angle 4.17392 ( 2271) link_ALPHA1-3 : bond 0.00192 ( 1) link_ALPHA1-3 : angle 3.60890 ( 3) link_ALPHA1-6 : bond 0.00049 ( 1) link_ALPHA1-6 : angle 1.89797 ( 3) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 1.77729 ( 6) link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 9.33993 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7845 (pt0) cc_final: 0.7563 (mt-10) REVERT: A 293 MET cc_start: 0.8589 (mmt) cc_final: 0.8351 (mmt) REVERT: A 935 TYR cc_start: 0.7730 (m-80) cc_final: 0.7457 (t80) REVERT: A 1195 HIS cc_start: 0.7416 (m-70) cc_final: 0.6905 (m-70) REVERT: A 1332 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7804 (ttt-90) REVERT: A 1377 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7333 (tp30) REVERT: A 1391 PHE cc_start: 0.6993 (m-80) cc_final: 0.6654 (t80) REVERT: A 1400 MET cc_start: 0.8510 (mtm) cc_final: 0.8049 (mtp) REVERT: A 1522 TRP cc_start: 0.8018 (t60) cc_final: 0.7542 (t60) REVERT: A 1672 MET cc_start: 0.8542 (ttp) cc_final: 0.8186 (tmm) REVERT: A 1793 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7658 (mtm180) outliers start: 20 outliers final: 18 residues processed: 154 average time/residue: 0.2904 time to fit residues: 65.5568 Evaluate side-chains 148 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 105 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074094 restraints weight = 74166.677| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.37 r_work: 0.2861 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14334 Z= 0.266 Angle : 0.585 16.885 19623 Z= 0.299 Chirality : 0.039 0.257 2241 Planarity : 0.004 0.056 2350 Dihedral : 9.315 61.654 3576 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.59 % Allowed : 10.85 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.21 (0.21), residues: 1639 helix: 2.50 (0.16), residues: 1015 sheet: 0.33 (0.66), residues: 60 loop : -0.36 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1504 TYR 0.011 0.001 TYR A1276 PHE 0.017 0.002 PHE A1180 TRP 0.010 0.001 TRP A 289 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00597 (14327) covalent geometry : angle 0.56939 (19604) SS BOND : bond 0.00646 ( 2) SS BOND : angle 1.21053 ( 4) hydrogen bonds : bond 0.05044 ( 768) hydrogen bonds : angle 4.40352 ( 2271) link_ALPHA1-3 : bond 0.00357 ( 1) link_ALPHA1-3 : angle 3.70891 ( 3) link_ALPHA1-6 : bond 0.00412 ( 1) link_ALPHA1-6 : angle 1.46203 ( 3) link_BETA1-4 : bond 0.00313 ( 2) link_BETA1-4 : angle 1.77741 ( 6) link_NAG-ASN : bond 0.00459 ( 1) link_NAG-ASN : angle 9.86041 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.686 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: A 283 GLU cc_start: 0.7891 (pt0) cc_final: 0.7622 (mt-10) REVERT: A 293 MET cc_start: 0.8594 (mmt) cc_final: 0.8350 (mmt) REVERT: A 1195 HIS cc_start: 0.7444 (m-70) cc_final: 0.6956 (m-70) REVERT: A 1332 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7799 (ttt-90) REVERT: A 1391 PHE cc_start: 0.7064 (m-80) cc_final: 0.6730 (t80) REVERT: A 1400 MET cc_start: 0.8506 (mtm) cc_final: 0.8033 (mtp) REVERT: A 1522 TRP cc_start: 0.8060 (t60) cc_final: 0.7585 (t60) REVERT: A 1672 MET cc_start: 0.8595 (ttp) cc_final: 0.8224 (tmm) REVERT: A 1793 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7580 (mtm180) outliers start: 21 outliers final: 19 residues processed: 146 average time/residue: 0.2928 time to fit residues: 62.6860 Evaluate side-chains 146 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076536 restraints weight = 73470.149| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.40 r_work: 0.2905 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14334 Z= 0.114 Angle : 0.509 16.217 19623 Z= 0.252 Chirality : 0.036 0.237 2241 Planarity : 0.004 0.047 2350 Dihedral : 8.986 58.360 3576 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.06 % Allowed : 11.76 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.47 (0.21), residues: 1639 helix: 2.68 (0.16), residues: 1012 sheet: 0.51 (0.67), residues: 60 loop : -0.19 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 134 TYR 0.011 0.001 TYR A1800 PHE 0.018 0.001 PHE A1203 TRP 0.008 0.001 TRP A 224 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00250 (14327) covalent geometry : angle 0.49215 (19604) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.78536 ( 4) hydrogen bonds : bond 0.04482 ( 768) hydrogen bonds : angle 4.08089 ( 2271) link_ALPHA1-3 : bond 0.00003 ( 1) link_ALPHA1-3 : angle 3.36020 ( 3) link_ALPHA1-6 : bond 0.00185 ( 1) link_ALPHA1-6 : angle 1.61418 ( 3) link_BETA1-4 : bond 0.00289 ( 2) link_BETA1-4 : angle 1.69668 ( 6) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 9.39090 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7827 (pt0) cc_final: 0.7567 (mt-10) REVERT: A 293 MET cc_start: 0.8580 (mmt) cc_final: 0.8353 (mmt) REVERT: A 935 TYR cc_start: 0.7740 (m-80) cc_final: 0.7519 (t80) REVERT: A 1195 HIS cc_start: 0.7401 (m-70) cc_final: 0.6931 (m-70) REVERT: A 1332 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7792 (ttt-90) REVERT: A 1377 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7347 (tp30) REVERT: A 1391 PHE cc_start: 0.7014 (m-80) cc_final: 0.6671 (t80) REVERT: A 1400 MET cc_start: 0.8520 (mtm) cc_final: 0.8034 (mtp) REVERT: A 1522 TRP cc_start: 0.7937 (t60) cc_final: 0.7484 (t60) REVERT: A 1672 MET cc_start: 0.8488 (ttp) cc_final: 0.8186 (tmm) REVERT: A 1793 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7588 (mtm180) outliers start: 14 outliers final: 14 residues processed: 147 average time/residue: 0.2881 time to fit residues: 62.1735 Evaluate side-chains 145 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1737 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.075921 restraints weight = 73818.436| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.41 r_work: 0.2890 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14334 Z= 0.160 Angle : 0.520 16.563 19623 Z= 0.259 Chirality : 0.036 0.235 2241 Planarity : 0.004 0.052 2350 Dihedral : 8.797 59.497 3576 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.14 % Allowed : 11.84 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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 (0.21), residues: 1639 helix: 2.71 (0.16), residues: 1011 sheet: 0.35 (0.67), residues: 60 loop : -0.18 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.011 0.001 TYR A1800 PHE 0.014 0.001 PHE A1203 TRP 0.009 0.001 TRP A 289 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00358 (14327) covalent geometry : angle 0.50364 (19604) SS BOND : bond 0.00447 ( 2) SS BOND : angle 0.81955 ( 4) hydrogen bonds : bond 0.04486 ( 768) hydrogen bonds : angle 4.11784 ( 2271) link_ALPHA1-3 : bond 0.00126 ( 1) link_ALPHA1-3 : angle 3.41065 ( 3) link_ALPHA1-6 : bond 0.00270 ( 1) link_ALPHA1-6 : angle 1.61993 ( 3) link_BETA1-4 : bond 0.00286 ( 2) link_BETA1-4 : angle 1.75179 ( 6) link_NAG-ASN : bond 0.00286 ( 1) link_NAG-ASN : angle 9.62822 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7886 (pt0) cc_final: 0.7651 (mt-10) REVERT: A 293 MET cc_start: 0.8597 (mmt) cc_final: 0.8342 (mmt) REVERT: A 935 TYR cc_start: 0.7760 (m-80) cc_final: 0.7474 (t80) REVERT: A 1195 HIS cc_start: 0.7450 (m-70) cc_final: 0.6976 (m-70) REVERT: A 1377 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7322 (tp30) REVERT: A 1391 PHE cc_start: 0.7011 (m-80) cc_final: 0.6668 (t80) REVERT: A 1400 MET cc_start: 0.8527 (mtm) cc_final: 0.8047 (mtp) REVERT: A 1522 TRP cc_start: 0.7904 (t60) cc_final: 0.7413 (t60) REVERT: A 1672 MET cc_start: 0.8526 (ttp) cc_final: 0.8196 (tmm) outliers start: 15 outliers final: 15 residues processed: 142 average time/residue: 0.2674 time to fit residues: 56.3325 Evaluate side-chains 141 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1192 HIS Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1593 ASP Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1737 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 152 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 chunk 156 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077844 restraints weight = 72695.519| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.42 r_work: 0.2925 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14334 Z= 0.097 Angle : 0.483 16.096 19623 Z= 0.238 Chirality : 0.036 0.216 2241 Planarity : 0.003 0.039 2350 Dihedral : 8.518 57.928 3576 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.83 % Allowed : 12.22 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.68 (0.21), residues: 1639 helix: 2.82 (0.16), residues: 1014 sheet: 0.44 (0.68), residues: 60 loop : -0.02 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 134 TYR 0.012 0.001 TYR A1800 PHE 0.016 0.001 PHE A1203 TRP 0.008 0.001 TRP A 289 HIS 0.003 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00209 (14327) covalent geometry : angle 0.46599 (19604) SS BOND : bond 0.00296 ( 2) SS BOND : angle 0.51297 ( 4) hydrogen bonds : bond 0.04095 ( 768) hydrogen bonds : angle 3.91834 ( 2271) link_ALPHA1-3 : bond 0.00001 ( 1) link_ALPHA1-3 : angle 3.17687 ( 3) link_ALPHA1-6 : bond 0.00400 ( 1) link_ALPHA1-6 : angle 1.63931 ( 3) link_BETA1-4 : bond 0.00327 ( 2) link_BETA1-4 : angle 1.69806 ( 6) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 9.31590 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3278 Ramachandran restraints generated. 1639 Oldfield, 0 Emsley, 1639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue TYR 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue THR 556 is missing expected H atoms. Skipping. Residue VAL 557 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue ILE 715 is missing expected H atoms. Skipping. Residue LEU 716 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue SER 782 is missing expected H atoms. Skipping. Residue ILE 784 is missing expected H atoms. Skipping. Residue LYS 787 is missing expected H atoms. Skipping. Residue THR 806 is missing expected H atoms. Skipping. Residue SER 868 is missing expected H atoms. Skipping. Residue ILE 893 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue LYS 1172 is missing expected H atoms. Skipping. Residue THR 1175 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue VAL 1339 is missing expected H atoms. Skipping. Residue SER 1396 is missing expected H atoms. Skipping. Residue TYR 1424 is missing expected H atoms. Skipping. Residue ILE 1425 is missing expected H atoms. Skipping. Residue SER 1426 is missing expected H atoms. Skipping. Residue THR 1433 is missing expected H atoms. Skipping. Residue SER 1434 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1623 is missing expected H atoms. Skipping. Residue SER 1624 is missing expected H atoms. Skipping. Residue LYS 1637 is missing expected H atoms. Skipping. Residue THR 1638 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue ILE 1784 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASP cc_start: 0.7872 (m-30) cc_final: 0.7659 (m-30) REVERT: A 283 GLU cc_start: 0.7773 (pt0) cc_final: 0.7535 (mt-10) REVERT: A 293 MET cc_start: 0.8593 (mmt) cc_final: 0.8342 (mmt) REVERT: A 694 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 935 TYR cc_start: 0.7745 (m-80) cc_final: 0.7449 (t80) REVERT: A 1195 HIS cc_start: 0.7385 (m-70) cc_final: 0.6881 (m-70) REVERT: A 1377 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7378 (tp30) REVERT: A 1391 PHE cc_start: 0.7025 (m-80) cc_final: 0.6664 (t80) REVERT: A 1400 MET cc_start: 0.8531 (mtm) cc_final: 0.8050 (mtp) REVERT: A 1522 TRP cc_start: 0.7823 (t60) cc_final: 0.7359 (t60) REVERT: A 1672 MET cc_start: 0.8486 (ttp) cc_final: 0.8180 (tmm) outliers start: 11 outliers final: 10 residues processed: 145 average time/residue: 0.2610 time to fit residues: 56.8672 Evaluate side-chains 137 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1737 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.110247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080206 restraints weight = 72785.970| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.33 r_work: 0.2910 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14334 Z= 0.152 Angle : 0.503 16.435 19623 Z= 0.251 Chirality : 0.036 0.216 2241 Planarity : 0.003 0.043 2350 Dihedral : 8.469 59.256 3576 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.06 % Allowed : 11.99 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 2.66 (0.21), residues: 1639 helix: 2.81 (0.16), residues: 1015 sheet: 0.27 (0.67), residues: 60 loop : -0.03 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.011 0.001 TYR A1800 PHE 0.013 0.001 PHE A1203 TRP 0.009 0.001 TRP A 695 HIS 0.003 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00340 (14327) covalent geometry : angle 0.48576 (19604) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.64158 ( 4) hydrogen bonds : bond 0.04262 ( 768) hydrogen bonds : angle 4.01139 ( 2271) link_ALPHA1-3 : bond 0.00073 ( 1) link_ALPHA1-3 : angle 3.19746 ( 3) link_ALPHA1-6 : bond 0.00268 ( 1) link_ALPHA1-6 : angle 1.65639 ( 3) link_BETA1-4 : bond 0.00280 ( 2) link_BETA1-4 : angle 1.75602 ( 6) link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 9.54781 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5646.02 seconds wall clock time: 96 minutes 50.48 seconds (5810.48 seconds total)