Starting phenix.real_space_refine on Sun Feb 8 00:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i1j_52571/02_2026/9i1j_52571.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 7 5.49 5 Mg 1 5.21 5 S 215 5.16 5 C 23433 2.51 5 N 6316 2.21 5 O 6819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36793 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 35465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4423, 35465 Classifications: {'peptide': 4423} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 184, 'TRANS': 4237} Chain breaks: 14 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 138} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26376 SG CYS A3947 81.234 131.400 223.149 1.00409.99 S ATOM 26401 SG CYS A3950 79.023 127.942 221.287 1.00378.64 S ATOM 26529 SG CYS A3967 79.312 130.751 219.379 1.00484.47 S ATOM 26554 SG CYS A3970 77.771 131.570 223.068 1.00505.52 S ATOM 26486 SG CYS A3962 91.489 137.186 223.794 1.00512.10 S ATOM 26675 SG CYS A3985 93.453 135.515 227.098 1.00505.94 S Time building chain proxies: 7.92, per 1000 atoms: 0.22 Number of scatterers: 36793 At special positions: 0 Unit cell: (127.44, 158.12, 250.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 215 16.00 P 7 15.00 Mg 1 11.99 O 6819 8.00 N 6316 7.00 C 23433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3947 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3970 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3985 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3962 " Number of angles added : 6 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8762 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 18 sheets defined 61.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 504 through 513 removed outlier: 3.620A pdb=" N LEU A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 535 Processing helix chain 'A' and resid 558 through 575 removed outlier: 3.892A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 569 " --> pdb=" O HIS A 565 " (cutoff:3.500A) Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 578 through 582 removed outlier: 4.001A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.926A pdb=" N LEU A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 4.056A pdb=" N ASP A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 4.066A pdb=" N HIS A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 removed outlier: 3.958A pdb=" N ARG A 640 " --> pdb=" O PRO A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 642 through 656 removed outlier: 3.512A pdb=" N ARG A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 666 removed outlier: 3.692A pdb=" N GLY A 666 " --> pdb=" O ARG A 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 666' Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.975A pdb=" N CYS A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.636A pdb=" N TRP A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.898A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 724 removed outlier: 3.834A pdb=" N LEU A 724 " --> pdb=" O MET A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 724' Processing helix chain 'A' and resid 728 through 738 removed outlier: 4.392A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 4.304A pdb=" N SER A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N SER A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 759 through 775 removed outlier: 4.191A pdb=" N ASP A 763 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 781 through 801 removed outlier: 4.544A pdb=" N TYR A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 807 removed outlier: 4.113A pdb=" N ILE A 805 " --> pdb=" O GLN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 827 Processing helix chain 'A' and resid 835 through 851 Processing helix chain 'A' and resid 864 through 889 removed outlier: 3.669A pdb=" N PHE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 915 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.992A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 982 Processing helix chain 'A' and resid 994 through 1010 removed outlier: 3.589A pdb=" N PHE A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1031 through 1044 removed outlier: 4.165A pdb=" N ARG A1035 " --> pdb=" O TRP A1031 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1075 removed outlier: 3.509A pdb=" N GLU A1074 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1089 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1113 through 1144 removed outlier: 4.173A pdb=" N VAL A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1166 through 1171 removed outlier: 4.004A pdb=" N ASN A1169 " --> pdb=" O LYS A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1203 Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1219 through 1221 No H-bonds generated for 'chain 'A' and resid 1219 through 1221' Processing helix chain 'A' and resid 1233 through 1241 removed outlier: 3.870A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.598A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1276 through 1291 removed outlier: 3.732A pdb=" N LEU A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A1291 " --> pdb=" O MET A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1330 removed outlier: 4.422A pdb=" N GLY A1330 " --> pdb=" O ARG A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1347 removed outlier: 3.682A pdb=" N SER A1347 " --> pdb=" O ASN A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1362 No H-bonds generated for 'chain 'A' and resid 1360 through 1362' Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'A' and resid 1377 through 1387 Processing helix chain 'A' and resid 1387 through 1398 removed outlier: 4.100A pdb=" N VAL A1391 " --> pdb=" O GLN A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1415 removed outlier: 3.741A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1441 removed outlier: 4.172A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1463 Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1478 through 1484 Processing helix chain 'A' and resid 1497 through 1507 Processing helix chain 'A' and resid 1545 through 1557 removed outlier: 3.577A pdb=" N LEU A1557 " --> pdb=" O ASN A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 3.860A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1661 removed outlier: 3.956A pdb=" N LEU A1634 " --> pdb=" O ASP A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 3.869A pdb=" N ARG A1679 " --> pdb=" O SER A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1692 Processing helix chain 'A' and resid 1699 through 1708 Processing helix chain 'A' and resid 1712 through 1731 removed outlier: 3.655A pdb=" N ARG A1716 " --> pdb=" O SER A1712 " (cutoff:3.500A) Proline residue: A1727 - end of helix Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 3.794A pdb=" N LYS A1739 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1775 Processing helix chain 'A' and resid 1801 through 1811 Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 3.639A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1862 removed outlier: 3.516A pdb=" N LEU A1862 " --> pdb=" O ALA A1859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1881 removed outlier: 3.670A pdb=" N ALA A1881 " --> pdb=" O LEU A1877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1904 Processing helix chain 'A' and resid 1917 through 1930 Processing helix chain 'A' and resid 1938 through 1942 Processing helix chain 'A' and resid 1959 through 1974 Processing helix chain 'A' and resid 1993 through 2002 removed outlier: 4.266A pdb=" N VAL A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2005 No H-bonds generated for 'chain 'A' and resid 2003 through 2005' Processing helix chain 'A' and resid 2027 through 2037 Processing helix chain 'A' and resid 2081 through 2085 Processing helix chain 'A' and resid 2095 through 2100 Processing helix chain 'A' and resid 2116 through 2122 Processing helix chain 'A' and resid 2122 through 2137 Proline residue: A2128 - end of helix removed outlier: 3.842A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2165 removed outlier: 3.650A pdb=" N CYS A2158 " --> pdb=" O SER A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2193 removed outlier: 3.827A pdb=" N LEU A2176 " --> pdb=" O SER A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2203 Processing helix chain 'A' and resid 2207 through 2224 removed outlier: 3.622A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2319 removed outlier: 4.374A pdb=" N PHE A2312 " --> pdb=" O THR A2308 " (cutoff:3.500A) Processing helix chain 'A' and resid 2325 through 2329 removed outlier: 3.828A pdb=" N ASN A2328 " --> pdb=" O ASP A2325 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A2329 " --> pdb=" O PHE A2326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2325 through 2329' Processing helix chain 'A' and resid 2330 through 2342 Processing helix chain 'A' and resid 2357 through 2374 Processing helix chain 'A' and resid 2387 through 2400 Processing helix chain 'A' and resid 2417 through 2440 removed outlier: 3.502A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2465 removed outlier: 3.506A pdb=" N ILE A2462 " --> pdb=" O CYS A2458 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A2463 " --> pdb=" O ILE A2459 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A2465 " --> pdb=" O GLU A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2501 Processing helix chain 'A' and resid 2536 through 2540 Processing helix chain 'A' and resid 2550 through 2563 Processing helix chain 'A' and resid 2564 through 2568 removed outlier: 4.543A pdb=" N SER A2567 " --> pdb=" O ASP A2564 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A2568 " --> pdb=" O SER A2565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2564 through 2568' Processing helix chain 'A' and resid 2571 through 2589 removed outlier: 4.016A pdb=" N VAL A2575 " --> pdb=" O SER A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2615 removed outlier: 3.626A pdb=" N ARG A2604 " --> pdb=" O ARG A2600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A2607 " --> pdb=" O GLU A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2631 Processing helix chain 'A' and resid 2632 through 2636 removed outlier: 3.593A pdb=" N HIS A2635 " --> pdb=" O ASP A2632 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2654 removed outlier: 3.784A pdb=" N SER A2645 " --> pdb=" O PRO A2641 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A2646 " --> pdb=" O VAL A2642 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2669 removed outlier: 3.795A pdb=" N TYR A2664 " --> pdb=" O GLU A2660 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2672 No H-bonds generated for 'chain 'A' and resid 2670 through 2672' Processing helix chain 'A' and resid 2673 through 2677 Processing helix chain 'A' and resid 2678 through 2697 Processing helix chain 'A' and resid 2706 through 2722 Processing helix chain 'A' and resid 2736 through 2747 Processing helix chain 'A' and resid 2754 through 2759 removed outlier: 3.599A pdb=" N CYS A2759 " --> pdb=" O GLU A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2775 through 2791 removed outlier: 3.662A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2856 Processing helix chain 'A' and resid 2867 through 2879 Processing helix chain 'A' and resid 2883 through 2888 Processing helix chain 'A' and resid 2892 through 2907 removed outlier: 3.551A pdb=" N GLN A2907 " --> pdb=" O VAL A2903 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2932 removed outlier: 3.554A pdb=" N TYR A2917 " --> pdb=" O GLY A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2948 Processing helix chain 'A' and resid 2955 through 2964 Processing helix chain 'A' and resid 2965 through 2968 Processing helix chain 'A' and resid 2974 through 2984 removed outlier: 3.632A pdb=" N LEU A2978 " --> pdb=" O SER A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3018 removed outlier: 3.683A pdb=" N ILE A3014 " --> pdb=" O VAL A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3056 Processing helix chain 'A' and resid 3071 through 3077 removed outlier: 3.729A pdb=" N GLN A3077 " --> pdb=" O ASP A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3113 through 3120 Processing helix chain 'A' and resid 3122 through 3128 Processing helix chain 'A' and resid 3140 through 3159 Processing helix chain 'A' and resid 3172 through 3177 Processing helix chain 'A' and resid 3183 through 3197 removed outlier: 3.823A pdb=" N SER A3187 " --> pdb=" O ASP A3183 " (cutoff:3.500A) Processing helix chain 'A' and resid 3204 through 3219 removed outlier: 4.182A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3222 through 3229 Processing helix chain 'A' and resid 3230 through 3232 No H-bonds generated for 'chain 'A' and resid 3230 through 3232' Processing helix chain 'A' and resid 3236 through 3248 Processing helix chain 'A' and resid 3254 through 3264 removed outlier: 3.896A pdb=" N ARG A3264 " --> pdb=" O GLN A3260 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3296 removed outlier: 4.319A pdb=" N ASP A3290 " --> pdb=" O GLY A3286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3309 through 3311 No H-bonds generated for 'chain 'A' and resid 3309 through 3311' Processing helix chain 'A' and resid 3313 through 3327 removed outlier: 3.960A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A3327 " --> pdb=" O SER A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3349 through 3365 Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.666A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3422 through 3427 Processing helix chain 'A' and resid 3476 through 3491 removed outlier: 4.789A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3511 Processing helix chain 'A' and resid 3517 through 3540 removed outlier: 3.729A pdb=" N GLU A3540 " --> pdb=" O ASN A3536 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3556 Processing helix chain 'A' and resid 3556 through 3563 Processing helix chain 'A' and resid 3565 through 3590 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3594 through 3600 removed outlier: 4.219A pdb=" N LEU A3598 " --> pdb=" O ASN A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.109A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3676 removed outlier: 3.644A pdb=" N ILE A3661 " --> pdb=" O PHE A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3692 removed outlier: 3.523A pdb=" N THR A3692 " --> pdb=" O ILE A3688 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3699 Processing helix chain 'A' and resid 3702 through 3722 Processing helix chain 'A' and resid 3727 through 3746 Processing helix chain 'A' and resid 3753 through 3757 removed outlier: 3.635A pdb=" N LYS A3756 " --> pdb=" O GLU A3753 " (cutoff:3.500A) Processing helix chain 'A' and resid 3760 through 3785 removed outlier: 4.386A pdb=" N VAL A3764 " --> pdb=" O SER A3760 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS A3765 " --> pdb=" O LEU A3761 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS A3785 " --> pdb=" O ILE A3781 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.064A pdb=" N SER A3790 " --> pdb=" O PRO A3786 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A3794 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3824 Processing helix chain 'A' and resid 3828 through 3838 Processing helix chain 'A' and resid 3839 through 3847 removed outlier: 3.886A pdb=" N LEU A3843 " --> pdb=" O LEU A3839 " (cutoff:3.500A) Processing helix chain 'A' and resid 3856 through 3890 removed outlier: 4.379A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3894 through 3909 removed outlier: 3.782A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3940 removed outlier: 4.291A pdb=" N PHE A3921 " --> pdb=" O THR A3917 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3975 Processing helix chain 'A' and resid 4000 through 4027 Processing helix chain 'A' and resid 4035 through 4045 removed outlier: 4.026A pdb=" N ILE A4039 " --> pdb=" O GLU A4035 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4089 Processing helix chain 'A' and resid 4092 through 4095 Processing helix chain 'A' and resid 4096 through 4111 removed outlier: 3.533A pdb=" N ILE A4100 " --> pdb=" O VAL A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4116 through 4139 removed outlier: 4.353A pdb=" N LEU A4120 " --> pdb=" O ASP A4116 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4156 removed outlier: 3.874A pdb=" N VAL A4146 " --> pdb=" O ASN A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4160 through 4165 removed outlier: 3.651A pdb=" N GLY A4163 " --> pdb=" O GLY A4160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A4164 " --> pdb=" O LEU A4161 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A4165 " --> pdb=" O GLN A4162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4160 through 4165' Processing helix chain 'A' and resid 4171 through 4197 Processing helix chain 'A' and resid 4204 through 4219 Processing helix chain 'A' and resid 4222 through 4236 Processing helix chain 'A' and resid 4237 through 4245 removed outlier: 3.679A pdb=" N VAL A4241 " --> pdb=" O GLY A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4255 removed outlier: 4.046A pdb=" N VAL A4254 " --> pdb=" O CYS A4251 " (cutoff:3.500A) Processing helix chain 'A' and resid 4271 through 4276 removed outlier: 3.723A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A4276 " --> pdb=" O TYR A4273 " (cutoff:3.500A) Processing helix chain 'A' and resid 4279 through 4293 Processing helix chain 'A' and resid 4296 through 4305 removed outlier: 4.040A pdb=" N GLY A4300 " --> pdb=" O THR A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4309 through 4331 Processing helix chain 'A' and resid 4332 through 4335 removed outlier: 3.565A pdb=" N SER A4335 " --> pdb=" O PRO A4332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4332 through 4335' Processing helix chain 'A' and resid 4342 through 4353 Processing helix chain 'A' and resid 4358 through 4370 removed outlier: 3.865A pdb=" N ASP A4370 " --> pdb=" O ARG A4366 " (cutoff:3.500A) Processing helix chain 'A' and resid 4385 through 4403 Processing helix chain 'A' and resid 4405 through 4407 No H-bonds generated for 'chain 'A' and resid 4405 through 4407' Processing helix chain 'A' and resid 4408 through 4417 Processing helix chain 'A' and resid 4418 through 4422 removed outlier: 3.584A pdb=" N ALA A4422 " --> pdb=" O VAL A4419 " (cutoff:3.500A) Processing helix chain 'A' and resid 4522 through 4544 Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 3.935A pdb=" N LEU A4548 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4581 through 4596 Processing helix chain 'A' and resid 4613 through 4633 Processing helix chain 'A' and resid 4638 through 4648 Processing helix chain 'A' and resid 4655 through 4660 removed outlier: 4.193A pdb=" N LYS A4659 " --> pdb=" O ASN A4655 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A4660 " --> pdb=" O PRO A4656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4655 through 4660' Processing helix chain 'A' and resid 4691 through 4702 Processing helix chain 'A' and resid 4708 through 4717 removed outlier: 4.047A pdb=" N TRP A4712 " --> pdb=" O VAL A4708 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A4717 " --> pdb=" O HIS A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4722 Processing helix chain 'A' and resid 4723 through 4725 No H-bonds generated for 'chain 'A' and resid 4723 through 4725' Processing helix chain 'A' and resid 4726 through 4741 Processing helix chain 'A' and resid 4751 through 4758 Processing helix chain 'A' and resid 4761 through 4783 Processing helix chain 'A' and resid 4785 through 4790 Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 4.422A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4854 through 4858 removed outlier: 4.201A pdb=" N GLU A4857 " --> pdb=" O ASP A4854 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A4858 " --> pdb=" O ILE A4855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4854 through 4858' Processing helix chain 'A' and resid 4871 through 4878 Processing helix chain 'A' and resid 4895 through 4905 Processing helix chain 'A' and resid 4916 through 4919 removed outlier: 3.814A pdb=" N ILE A4919 " --> pdb=" O LEU A4916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4916 through 4919' Processing helix chain 'A' and resid 4930 through 4941 removed outlier: 3.534A pdb=" N PHE A4934 " --> pdb=" O TYR A4930 " (cutoff:3.500A) Processing helix chain 'A' and resid 4947 through 4958 Processing helix chain 'A' and resid 4960 through 4980 removed outlier: 3.650A pdb=" N THR A4980 " --> pdb=" O GLY A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 4988 through 4996 Processing helix chain 'A' and resid 5003 through 5011 removed outlier: 3.734A pdb=" N LEU A5007 " --> pdb=" O THR A5003 " (cutoff:3.500A) Processing helix chain 'A' and resid 5012 through 5013 No H-bonds generated for 'chain 'A' and resid 5012 through 5013' Processing helix chain 'A' and resid 5014 through 5016 No H-bonds generated for 'chain 'A' and resid 5014 through 5016' Processing helix chain 'A' and resid 5017 through 5036 Processing helix chain 'A' and resid 5045 through 5049 Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.122A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 4.224A pdb=" N LEU A5082 " --> pdb=" O GLU A5078 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A5083 " --> pdb=" O MET A5079 " (cutoff:3.500A) Processing helix chain 'A' and resid 5098 through 5108 removed outlier: 4.103A pdb=" N GLU A5108 " --> pdb=" O VAL A5104 " (cutoff:3.500A) Processing helix chain 'A' and resid 5115 through 5120 Processing helix chain 'A' and resid 5131 through 5147 Processing helix chain 'B' and resid 1 through 18 removed outlier: 3.851A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 1541 through 1544 removed outlier: 3.508A pdb=" N ARG A1541 " --> pdb=" O LEU A1530 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A1625 " --> pdb=" O MET A1615 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1793 through 1796 removed outlier: 6.438A pdb=" N ASN A1793 " --> pdb=" O ILE A1890 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A1892 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A1795 " --> pdb=" O CYS A1892 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR A1854 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU A1891 " --> pdb=" O TYR A1854 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A1856 " --> pdb=" O LEU A1891 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2058 through 2062 removed outlier: 6.416A pdb=" N GLY A1949 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A2061 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A1951 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1984 through 1987 Processing sheet with id=AA5, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id=AA7, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id=AA8, first strand: chain 'A' and resid 2377 through 2379 removed outlier: 4.520A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A2445 " --> pdb=" O ILE A2482 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA A2484 " --> pdb=" O LEU A2445 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A2447 " --> pdb=" O ALA A2484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB1, first strand: chain 'A' and resid 2762 through 2767 removed outlier: 5.647A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY A2841 " --> pdb=" O TYR A2798 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER A2800 " --> pdb=" O GLY A2841 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A2843 " --> pdb=" O SER A2800 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A2802 " --> pdb=" O VAL A2843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 3002 through 3006 removed outlier: 6.581A pdb=" N LEU A3002 " --> pdb=" O VAL A3109 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLU A3111 " --> pdb=" O LEU A3002 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL A3004 " --> pdb=" O GLU A3111 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 3086 through 3092 removed outlier: 4.409A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A3095 " --> pdb=" O LEU A3092 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 6.451A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A3373 " --> pdb=" O VAL A3273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3492 through 3493 Processing sheet with id=AB6, first strand: chain 'A' and resid 3958 through 3959 removed outlier: 3.572A pdb=" N VAL A3958 " --> pdb=" O TYR A3966 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4852 through 4853 Processing sheet with id=AB8, first strand: chain 'A' and resid 4880 through 4884 Processing sheet with id=AB9, first strand: chain 'B' and resid 22 through 28 removed outlier: 5.654A pdb=" N ASN B 24 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 38 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP B 28 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 34 " --> pdb=" O ASP B 28 " (cutoff:3.500A) 1857 hydrogen bonds defined for protein. 5472 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: 12.30 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11998 1.34 - 1.46: 6235 1.46 - 1.58: 19005 1.58 - 1.69: 11 1.69 - 1.81: 317 Bond restraints: 37566 Sorted by residual: bond pdb=" CA ASN A1050 " pdb=" CB ASN A1050 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.62e-02 3.81e+03 9.92e+00 bond pdb=" CB ASN A1995 " pdb=" CG ASN A1995 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.60e+00 bond pdb=" CG GLN A2557 " pdb=" CD GLN A2557 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.29e+00 bond pdb=" C THR A1988 " pdb=" N GLU A1989 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.59e-02 3.96e+03 2.30e+00 bond pdb=" N PRO A2321 " pdb=" CA PRO A2321 " ideal model delta sigma weight residual 1.469 1.487 -0.019 1.28e-02 6.10e+03 2.16e+00 ... (remaining 37561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 50142 2.57 - 5.14: 581 5.14 - 7.72: 97 7.72 - 10.29: 19 10.29 - 12.86: 4 Bond angle restraints: 50843 Sorted by residual: angle pdb=" N VAL A4604 " pdb=" CA VAL A4604 " pdb=" C VAL A4604 " ideal model delta sigma weight residual 112.29 106.97 5.32 9.40e-01 1.13e+00 3.21e+01 angle pdb=" C GLU A 748 " pdb=" N ASN A 749 " pdb=" CA ASN A 749 " ideal model delta sigma weight residual 122.65 113.40 9.25 1.66e+00 3.63e-01 3.10e+01 angle pdb=" CA GLN A3711 " pdb=" CB GLN A3711 " pdb=" CG GLN A3711 " ideal model delta sigma weight residual 114.10 124.64 -10.54 2.00e+00 2.50e-01 2.78e+01 angle pdb=" C LEU A2536 " pdb=" N ILE A2537 " pdb=" CA ILE A2537 " ideal model delta sigma weight residual 120.24 123.33 -3.09 6.30e-01 2.52e+00 2.40e+01 angle pdb=" C PRO A3121 " pdb=" N VAL A3122 " pdb=" CA VAL A3122 " ideal model delta sigma weight residual 122.13 130.70 -8.57 1.85e+00 2.92e-01 2.15e+01 ... (remaining 50838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.77: 20980 26.77 - 53.54: 1710 53.54 - 80.31: 156 80.31 - 107.08: 44 107.08 - 133.85: 3 Dihedral angle restraints: 22893 sinusoidal: 9437 harmonic: 13456 Sorted by residual: dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -142.29 -37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA ILE A 641 " pdb=" C ILE A 641 " pdb=" N ARG A 642 " pdb=" CA ARG A 642 " ideal model delta harmonic sigma weight residual -180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" C2' ADP A5206 " pdb=" C1' ADP A5206 " pdb=" N9 ADP A5206 " pdb=" C4 ADP A5206 " ideal model delta sinusoidal sigma weight residual 91.55 -134.60 -133.85 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 22890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4647 0.053 - 0.106: 934 0.106 - 0.160: 125 0.160 - 0.213: 12 0.213 - 0.266: 5 Chirality restraints: 5723 Sorted by residual: chirality pdb=" CB ILE A1373 " pdb=" CA ILE A1373 " pdb=" CG1 ILE A1373 " pdb=" CG2 ILE A1373 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB THR A1052 " pdb=" CA THR A1052 " pdb=" OG1 THR A1052 " pdb=" CG2 THR A1052 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU A2356 " pdb=" CB LEU A2356 " pdb=" CD1 LEU A2356 " pdb=" CD2 LEU A2356 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5720 not shown) Planarity restraints: 6498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A5023 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C GLN A5023 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN A5023 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A5024 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A3826 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO A3827 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A3827 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A3827 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2422 " 0.017 2.00e-02 2.50e+03 1.49e-02 4.45e+00 pdb=" CG TYR A2422 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A2422 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A2422 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A2422 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A2422 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A2422 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A2422 " 0.001 2.00e-02 2.50e+03 ... (remaining 6495 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 44 2.60 - 3.18: 32815 3.18 - 3.75: 59766 3.75 - 4.33: 77693 4.33 - 4.90: 125814 Nonbonded interactions: 296132 Sorted by model distance: nonbonded pdb=" O LEU A2599 " pdb=" O5' ADP A5205 " model vdw 2.031 3.040 nonbonded pdb=" O GLN A3707 " pdb=" OE1 GLN A3711 " model vdw 2.344 3.040 nonbonded pdb=" N ARG A2600 " pdb=" O1A ADP A5205 " model vdw 2.349 3.120 nonbonded pdb=" O4' ADP A5206 " pdb=" O5' ADP A5206 " model vdw 2.364 2.432 nonbonded pdb=" CG1 ILE A2558 " pdb=" O2' ADP A5205 " model vdw 2.389 3.440 ... (remaining 296127 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 44.230 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 0.879 37575 Z= 0.497 Angle : 0.755 23.410 50851 Z= 0.393 Chirality : 0.043 0.266 5723 Planarity : 0.004 0.070 6498 Dihedral : 18.082 133.849 14128 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 1.97 % Allowed : 25.25 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.12), residues: 4544 helix: 0.34 (0.10), residues: 2532 sheet: -1.53 (0.34), residues: 221 loop : -2.15 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A4998 TYR 0.037 0.001 TYR A2422 PHE 0.032 0.002 PHE A2925 TRP 0.028 0.002 TRP A2181 HIS 0.019 0.001 HIS A2413 Details of bonding type rmsd covalent geometry : bond 0.00309 (37566) covalent geometry : angle 0.73461 (50843) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.15101 ( 2) hydrogen bonds : bond 0.12285 ( 1857) hydrogen bonds : angle 5.70782 ( 5472) metal coordination : bond 0.29275 ( 7) metal coordination : angle 16.12962 ( 6) Misc. bond : bond 0.87925 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 872 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 565 HIS cc_start: 0.8882 (t70) cc_final: 0.8600 (m-70) REVERT: A 594 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5780 (pp) REVERT: A 644 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7205 (mtt180) REVERT: A 663 ARG cc_start: 0.6622 (mtt-85) cc_final: 0.6366 (mmm160) REVERT: A 795 MET cc_start: 0.5517 (mmp) cc_final: 0.4298 (mmt) REVERT: A 969 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7528 (pp20) REVERT: A 1350 ASP cc_start: 0.8761 (m-30) cc_final: 0.8378 (p0) REVERT: A 1550 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8791 (tm-30) REVERT: A 1554 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8241 (mtpp) REVERT: A 1579 ASN cc_start: 0.9118 (m-40) cc_final: 0.8786 (m-40) REVERT: A 1630 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7621 (t0) REVERT: A 1631 VAL cc_start: 0.7887 (t) cc_final: 0.7679 (p) REVERT: A 1644 ASP cc_start: 0.8835 (m-30) cc_final: 0.8115 (m-30) REVERT: A 1827 CYS cc_start: 0.8263 (m) cc_final: 0.7901 (m) REVERT: A 2039 GLN cc_start: 0.7651 (mt0) cc_final: 0.6074 (tt0) REVERT: A 2050 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7005 (tpt-90) REVERT: A 2115 MET cc_start: 0.3213 (mmm) cc_final: 0.2395 (mmm) REVERT: A 2290 TYR cc_start: 0.8334 (m-10) cc_final: 0.7854 (m-10) REVERT: A 2318 GLN cc_start: 0.7834 (mm-40) cc_final: 0.6925 (tt0) REVERT: A 2560 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7571 (pp30) REVERT: A 2587 MET cc_start: 0.8264 (mmt) cc_final: 0.7264 (ttt) REVERT: A 2607 LYS cc_start: 0.9422 (mttt) cc_final: 0.9186 (mmmt) REVERT: A 2672 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 2701 THR cc_start: 0.8683 (m) cc_final: 0.8211 (p) REVERT: A 2815 LYS cc_start: 0.7748 (mtmm) cc_final: 0.7279 (tptp) REVERT: A 2837 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7711 (t80) REVERT: A 2948 PHE cc_start: 0.8425 (m-80) cc_final: 0.8143 (m-80) REVERT: A 3010 VAL cc_start: 0.8904 (t) cc_final: 0.8332 (m) REVERT: A 3111 GLU cc_start: 0.8859 (tp30) cc_final: 0.8448 (tp30) REVERT: A 3208 LYS cc_start: 0.8409 (tttt) cc_final: 0.7384 (ttmt) REVERT: A 3276 GLU cc_start: 0.8391 (tt0) cc_final: 0.8041 (tt0) REVERT: A 3410 MET cc_start: 0.8605 (mpp) cc_final: 0.8183 (mtt) REVERT: A 3482 GLN cc_start: 0.9002 (mt0) cc_final: 0.8770 (mt0) REVERT: A 3509 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (mm) REVERT: A 3515 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6650 (tp30) REVERT: A 3529 MET cc_start: 0.7038 (tpt) cc_final: 0.6434 (mtp) REVERT: A 3679 GLU cc_start: 0.7341 (mp0) cc_final: 0.6980 (pm20) REVERT: A 3683 LYS cc_start: 0.8429 (ttpp) cc_final: 0.7962 (mmtt) REVERT: A 3728 GLU cc_start: 0.8623 (pm20) cc_final: 0.8040 (mp0) REVERT: A 3806 MET cc_start: 0.7468 (ppp) cc_final: 0.7241 (tmm) REVERT: A 3814 MET cc_start: 0.7192 (mmt) cc_final: 0.6917 (mtt) REVERT: A 3874 PHE cc_start: 0.9370 (t80) cc_final: 0.8749 (t80) REVERT: A 4025 THR cc_start: 0.8103 (p) cc_final: 0.7185 (t) REVERT: A 4026 MET cc_start: 0.7937 (tmm) cc_final: 0.7443 (mmt) REVERT: A 4029 LYS cc_start: 0.8988 (mtmt) cc_final: 0.8713 (tptt) REVERT: A 4322 TYR cc_start: 0.8660 (t80) cc_final: 0.8380 (t80) REVERT: A 4688 ARG cc_start: 0.5922 (mtm-85) cc_final: 0.5054 (mmp-170) REVERT: A 4713 HIS cc_start: 0.8913 (m90) cc_final: 0.8500 (m90) REVERT: A 4722 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7441 (ttm110) REVERT: A 4814 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.7235 (Cg_exo) REVERT: A 4835 ASN cc_start: 0.8234 (t0) cc_final: 0.7568 (m-40) REVERT: A 4856 SER cc_start: 0.8438 (m) cc_final: 0.8235 (m) REVERT: A 4949 LEU cc_start: 0.9145 (pt) cc_final: 0.8620 (pt) REVERT: A 5012 ARG cc_start: 0.8898 (ttm170) cc_final: 0.8383 (ttm170) REVERT: A 5125 GLU cc_start: 0.8336 (pt0) cc_final: 0.8128 (pm20) REVERT: A 5128 MET cc_start: 0.5915 (tpp) cc_final: 0.5351 (tpp) REVERT: B 93 GLU cc_start: 0.9424 (mp0) cc_final: 0.9013 (pm20) outliers start: 81 outliers final: 15 residues processed: 936 average time/residue: 0.2300 time to fit residues: 345.6580 Evaluate side-chains 526 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 504 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1248 ASN Chi-restraints excluded: chain A residue 1630 ASP Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2050 ARG Chi-restraints excluded: chain A residue 2223 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2560 GLN Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2672 PHE Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 4169 ILE Chi-restraints excluded: chain A residue 4965 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 676 GLN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A1129 GLN A1169 ASN ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN ** A1387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1849 GLN ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1995 ASN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2288 ASN A2298 ASN A2360 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2472 HIS A2557 GLN ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2905 GLN ** A2938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2955 GLN ** A3037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3045 ASN A3047 ASN A3065 GLN A3253 ASN A3541 ASN A3542 GLN ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3608 GLN A3653 ASN A3745 GLN ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3882 HIS A4249 HIS ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN ** A4879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4902 GLN A5005 GLN ** A5037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5047 GLN A5077 HIS A5094 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.093381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.076048 restraints weight = 217411.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.077862 restraints weight = 144539.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.079025 restraints weight = 103321.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.079851 restraints weight = 81648.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.080216 restraints weight = 68687.424| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 37575 Z= 0.266 Angle : 0.845 15.465 50851 Z= 0.421 Chirality : 0.047 0.321 5723 Planarity : 0.005 0.059 6498 Dihedral : 7.449 134.881 5037 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 5.48 % Allowed : 25.62 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4544 helix: 0.43 (0.10), residues: 2554 sheet: -1.56 (0.34), residues: 215 loop : -2.17 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A5145 TYR 0.033 0.002 TYR A2918 PHE 0.029 0.003 PHE A2371 TRP 0.025 0.003 TRP A2181 HIS 0.009 0.002 HIS A3785 Details of bonding type rmsd covalent geometry : bond 0.00560 (37566) covalent geometry : angle 0.83909 (50843) SS BOND : bond 0.08885 ( 1) SS BOND : angle 3.48367 ( 2) hydrogen bonds : bond 0.04263 ( 1857) hydrogen bonds : angle 4.90213 ( 5472) metal coordination : bond 0.00949 ( 7) metal coordination : angle 9.16033 ( 6) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 518 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ASN cc_start: 0.8623 (m-40) cc_final: 0.8422 (m110) REVERT: A 819 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6838 (mm) REVERT: A 969 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7498 (pp20) REVERT: A 1013 HIS cc_start: 0.7993 (t-90) cc_final: 0.7767 (t-90) REVERT: A 1026 LYS cc_start: 0.9329 (mmmt) cc_final: 0.8889 (tptt) REVERT: A 1152 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5971 (m-80) REVERT: A 1249 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5589 (t80) REVERT: A 1265 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9167 (pp20) REVERT: A 1286 PHE cc_start: 0.8975 (m-80) cc_final: 0.8736 (m-80) REVERT: A 1549 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8546 (mmmm) REVERT: A 1551 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 1579 ASN cc_start: 0.9046 (m-40) cc_final: 0.8749 (m-40) REVERT: A 1642 MET cc_start: 0.8597 (mmm) cc_final: 0.8163 (mmm) REVERT: A 1644 ASP cc_start: 0.8805 (m-30) cc_final: 0.8394 (m-30) REVERT: A 1744 MET cc_start: 0.9076 (mmt) cc_final: 0.8788 (mmp) REVERT: A 1746 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8539 (tp-100) REVERT: A 2115 MET cc_start: 0.4247 (mmm) cc_final: 0.3361 (mmm) REVERT: A 2276 MET cc_start: 0.8959 (mtp) cc_final: 0.8537 (mtm) REVERT: A 2318 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7006 (tt0) REVERT: A 2323 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 2449 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: A 2560 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7705 (pp30) REVERT: A 2587 MET cc_start: 0.8511 (mmt) cc_final: 0.7953 (ttm) REVERT: A 2701 THR cc_start: 0.9046 (m) cc_final: 0.8733 (p) REVERT: A 2837 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 2848 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.6614 (m100) REVERT: A 3008 ASN cc_start: 0.8634 (t0) cc_final: 0.8318 (t0) REVERT: A 3073 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: A 3150 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 3276 GLU cc_start: 0.8022 (tt0) cc_final: 0.7719 (tt0) REVERT: A 3404 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5384 (mt) REVERT: A 3482 GLN cc_start: 0.9052 (mt0) cc_final: 0.8541 (tm-30) REVERT: A 3509 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 3515 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6833 (tp30) REVERT: A 3539 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: A 3547 LYS cc_start: 0.7914 (mttt) cc_final: 0.7594 (mttm) REVERT: A 3553 GLU cc_start: 0.8610 (tp30) cc_final: 0.8369 (tp30) REVERT: A 3571 TRP cc_start: 0.8027 (t60) cc_final: 0.7706 (t-100) REVERT: A 3683 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8257 (mmtt) REVERT: A 3714 LEU cc_start: 0.9004 (tp) cc_final: 0.8508 (mm) REVERT: A 3715 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8437 (ptpp) REVERT: A 3719 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 3728 GLU cc_start: 0.8557 (pm20) cc_final: 0.8315 (mp0) REVERT: A 3774 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8013 (mtm180) REVERT: A 3819 MET cc_start: 0.7771 (ppp) cc_final: 0.7244 (ppp) REVERT: A 3925 MET cc_start: 0.8834 (ptm) cc_final: 0.8524 (ptt) REVERT: A 4086 LYS cc_start: 0.8963 (tttt) cc_final: 0.8696 (ptmt) REVERT: A 4238 MET cc_start: 0.7642 (tmm) cc_final: 0.7265 (tmm) REVERT: A 4322 TYR cc_start: 0.8757 (t80) cc_final: 0.8470 (t80) REVERT: A 4344 GLU cc_start: 0.8631 (pm20) cc_final: 0.8399 (pm20) REVERT: A 4500 GLN cc_start: 0.4450 (tp-100) cc_final: 0.4007 (mp-120) REVERT: A 4688 ARG cc_start: 0.5636 (mtm-85) cc_final: 0.4968 (mmp-170) REVERT: A 4713 HIS cc_start: 0.8871 (m90) cc_final: 0.8262 (m90) REVERT: A 4722 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7779 (ttm-80) REVERT: A 4729 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: A 4782 LEU cc_start: 0.9083 (tp) cc_final: 0.8838 (pp) REVERT: A 4835 ASN cc_start: 0.8080 (t0) cc_final: 0.7575 (m-40) REVERT: A 4901 ARG cc_start: 0.9100 (mmp80) cc_final: 0.8879 (mmp80) REVERT: A 5000 CYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7263 (t) REVERT: A 5012 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8384 (ttm170) REVERT: A 5074 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 5107 MET cc_start: 0.6964 (ppp) cc_final: 0.6128 (tmm) REVERT: A 5125 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: B 19 MET cc_start: 0.2731 (pmm) cc_final: 0.2514 (pmm) outliers start: 225 outliers final: 97 residues processed: 711 average time/residue: 0.2274 time to fit residues: 265.4622 Evaluate side-chains 532 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 415 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 718 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1031 TRP Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1248 ASN Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1451 PHE Chi-restraints excluded: chain A residue 1520 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1553 ASN Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1732 SER Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1966 THR Chi-restraints excluded: chain A residue 1995 ASN Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2044 ILE Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2218 LEU Chi-restraints excluded: chain A residue 2267 VAL Chi-restraints excluded: chain A residue 2286 ASN Chi-restraints excluded: chain A residue 2302 ILE Chi-restraints excluded: chain A residue 2323 ASN Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2429 GLU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2560 GLN Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2634 THR Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2743 VAL Chi-restraints excluded: chain A residue 2756 LEU Chi-restraints excluded: chain A residue 2763 VAL Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2848 TRP Chi-restraints excluded: chain A residue 2889 ILE Chi-restraints excluded: chain A residue 2973 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3150 LEU Chi-restraints excluded: chain A residue 3183 ASP Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3275 THR Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3506 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3539 GLU Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3578 VAL Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 4102 ASN Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4313 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4346 VAL Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4419 VAL Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4729 GLU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4824 THR Chi-restraints excluded: chain A residue 4848 ASP Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 5000 CYS Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain A residue 5125 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 39 optimal weight: 0.0770 chunk 391 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 373 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 418 optimal weight: 0.0370 chunk 297 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 407 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 392 optimal weight: 0.7980 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN A1129 GLN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 HIS A1429 HIS ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1655 GLN ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 GLN ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1995 ASN A2063 GLN ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2557 GLN A2560 GLN ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2905 GLN A3037 GLN A3045 ASN A3047 ASN A3250 GLN A3653 ASN A3690 GLN A3765 HIS ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3834 GLN ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 GLN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4759 HIS ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.095151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.078040 restraints weight = 212855.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.079930 restraints weight = 136459.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.081148 restraints weight = 96978.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.082006 restraints weight = 75889.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.082380 restraints weight = 63294.028| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37575 Z= 0.140 Angle : 0.743 12.754 50851 Z= 0.358 Chirality : 0.044 0.298 5723 Planarity : 0.004 0.052 6498 Dihedral : 6.957 136.128 5019 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 3.85 % Allowed : 26.03 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4544 helix: 0.59 (0.10), residues: 2574 sheet: -1.37 (0.34), residues: 215 loop : -2.12 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A4630 TYR 0.038 0.002 TYR A4316 PHE 0.032 0.002 PHE A 998 TRP 0.028 0.002 TRP A2181 HIS 0.013 0.001 HIS A3882 Details of bonding type rmsd covalent geometry : bond 0.00309 (37566) covalent geometry : angle 0.73801 (50843) SS BOND : bond 0.00057 ( 1) SS BOND : angle 2.67318 ( 2) hydrogen bonds : bond 0.03718 ( 1857) hydrogen bonds : angle 4.58771 ( 5472) metal coordination : bond 0.00214 ( 7) metal coordination : angle 7.71411 ( 6) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 471 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 644 ARG cc_start: 0.6083 (mtt180) cc_final: 0.5763 (mtt180) REVERT: A 795 MET cc_start: 0.5545 (mmp) cc_final: 0.5283 (mmp) REVERT: A 882 ARG cc_start: 0.9278 (ttp-170) cc_final: 0.9069 (ptp-110) REVERT: A 969 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7417 (pp20) REVERT: A 1026 LYS cc_start: 0.9323 (mmmt) cc_final: 0.8847 (tptt) REVERT: A 1189 LEU cc_start: 0.7098 (mp) cc_final: 0.6707 (pp) REVERT: A 1265 GLU cc_start: 0.9425 (mm-30) cc_final: 0.9119 (pp20) REVERT: A 1286 PHE cc_start: 0.9016 (m-80) cc_final: 0.8732 (m-80) REVERT: A 1579 ASN cc_start: 0.9058 (m-40) cc_final: 0.8761 (m-40) REVERT: A 1596 MET cc_start: 0.8477 (mpp) cc_final: 0.8194 (mpp) REVERT: A 1644 ASP cc_start: 0.8823 (m-30) cc_final: 0.8407 (m-30) REVERT: A 1744 MET cc_start: 0.8945 (mmt) cc_final: 0.8630 (mmt) REVERT: A 1746 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8290 (tp-100) REVERT: A 1810 TYR cc_start: 0.7160 (m-80) cc_final: 0.6180 (m-10) REVERT: A 1825 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6266 (tp) REVERT: A 1905 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 2115 MET cc_start: 0.4081 (mmm) cc_final: 0.3119 (mmm) REVERT: A 2179 PHE cc_start: 0.6998 (t80) cc_final: 0.6689 (t80) REVERT: A 2318 GLN cc_start: 0.7911 (mm-40) cc_final: 0.6990 (tt0) REVERT: A 2380 MET cc_start: 0.8613 (tpt) cc_final: 0.8353 (tpp) REVERT: A 2420 MET cc_start: 0.7367 (mtt) cc_final: 0.7121 (mtm) REVERT: A 2449 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5201 (pm20) REVERT: A 2587 MET cc_start: 0.8444 (mmt) cc_final: 0.7719 (ttm) REVERT: A 2701 THR cc_start: 0.8963 (m) cc_final: 0.8696 (p) REVERT: A 2837 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 2973 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7136 (p) REVERT: A 3047 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8874 (m110) REVERT: A 3073 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: A 3207 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7385 (tpm170) REVERT: A 3276 GLU cc_start: 0.8176 (tt0) cc_final: 0.7881 (tt0) REVERT: A 3410 MET cc_start: 0.8373 (mtm) cc_final: 0.8035 (mtt) REVERT: A 3482 GLN cc_start: 0.8986 (mt0) cc_final: 0.8485 (tm-30) REVERT: A 3509 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 3515 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6822 (tp30) REVERT: A 3529 MET cc_start: 0.6890 (tpt) cc_final: 0.6483 (mtt) REVERT: A 3553 GLU cc_start: 0.8554 (tp30) cc_final: 0.8244 (tp30) REVERT: A 3573 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6821 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8288 (mmtt) REVERT: A 3719 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8518 (mt) REVERT: A 3728 GLU cc_start: 0.8510 (pm20) cc_final: 0.8302 (mp0) REVERT: A 3774 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: A 3819 MET cc_start: 0.7895 (ppp) cc_final: 0.7322 (ppp) REVERT: A 3874 PHE cc_start: 0.9328 (t80) cc_final: 0.9125 (t80) REVERT: A 4238 MET cc_start: 0.7766 (tmm) cc_final: 0.7316 (tmm) REVERT: A 4322 TYR cc_start: 0.8774 (t80) cc_final: 0.8409 (t80) REVERT: A 4429 MET cc_start: 0.2989 (mmm) cc_final: 0.2756 (mmm) REVERT: A 4500 GLN cc_start: 0.4320 (tp-100) cc_final: 0.3971 (mp-120) REVERT: A 4688 ARG cc_start: 0.5594 (mtm-85) cc_final: 0.5037 (mmp-170) REVERT: A 4722 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7754 (ttm-80) REVERT: A 4729 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: A 4901 ARG cc_start: 0.9102 (mmp80) cc_final: 0.8878 (mmp80) REVERT: A 4972 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7783 (pp20) REVERT: A 5012 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8286 (ttm170) REVERT: A 5074 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8682 (mm) REVERT: B 19 MET cc_start: 0.3108 (pmm) cc_final: 0.2141 (pmm) outliers start: 158 outliers final: 70 residues processed: 597 average time/residue: 0.2318 time to fit residues: 227.7230 Evaluate side-chains 485 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 402 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1248 ASN Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1605 VAL Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1732 SER Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2044 ILE Chi-restraints excluded: chain A residue 2088 PHE Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2267 VAL Chi-restraints excluded: chain A residue 2302 ILE Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2973 VAL Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3047 ASN Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3092 LEU Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3183 ASP Chi-restraints excluded: chain A residue 3274 PHE Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3399 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3711 GLN Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3772 ARG Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4419 VAL Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4607 PHE Chi-restraints excluded: chain A residue 4676 SER Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4729 GLU Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain B residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 371 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 431 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 238 optimal weight: 0.0970 chunk 442 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 GLN ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2790 GLN A3047 ASN A3095 HIS A3653 ASN ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4834 HIS ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.078460 restraints weight = 209170.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.080374 restraints weight = 135523.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.081602 restraints weight = 96564.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.082500 restraints weight = 75581.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.082881 restraints weight = 62865.104| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37575 Z= 0.130 Angle : 0.729 12.499 50851 Z= 0.349 Chirality : 0.044 0.302 5723 Planarity : 0.004 0.060 6498 Dihedral : 6.766 135.348 5015 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.78 % Favored : 93.18 % Rotamer: Outliers : 3.39 % Allowed : 26.42 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4544 helix: 0.69 (0.10), residues: 2562 sheet: -1.26 (0.33), residues: 241 loop : -2.12 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1327 TYR 0.030 0.001 TYR A4316 PHE 0.026 0.001 PHE A2393 TRP 0.028 0.002 TRP A2346 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00284 (37566) covalent geometry : angle 0.72572 (50843) SS BOND : bond 0.00205 ( 1) SS BOND : angle 1.49805 ( 2) hydrogen bonds : bond 0.03626 ( 1857) hydrogen bonds : angle 4.47634 ( 5472) metal coordination : bond 0.00182 ( 7) metal coordination : angle 6.44257 ( 6) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 451 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 795 MET cc_start: 0.5450 (mmp) cc_final: 0.5143 (mmp) REVERT: A 819 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6912 (mm) REVERT: A 882 ARG cc_start: 0.9240 (ttp-170) cc_final: 0.9012 (ptp-110) REVERT: A 969 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7425 (pp20) REVERT: A 1047 ILE cc_start: 0.8770 (mp) cc_final: 0.8262 (tp) REVERT: A 1189 LEU cc_start: 0.7305 (mp) cc_final: 0.6868 (pp) REVERT: A 1265 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9120 (pp20) REVERT: A 1286 PHE cc_start: 0.8895 (m-80) cc_final: 0.8627 (m-80) REVERT: A 1551 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 1558 MET cc_start: 0.7305 (ppp) cc_final: 0.6950 (ppp) REVERT: A 1579 ASN cc_start: 0.9037 (m-40) cc_final: 0.8726 (m-40) REVERT: A 1602 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 1644 ASP cc_start: 0.8784 (m-30) cc_final: 0.8381 (m-30) REVERT: A 1689 MET cc_start: 0.7993 (mmp) cc_final: 0.6819 (ttp) REVERT: A 1744 MET cc_start: 0.8901 (mmt) cc_final: 0.8597 (mmt) REVERT: A 1746 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8181 (tp-100) REVERT: A 1810 TYR cc_start: 0.7046 (m-80) cc_final: 0.6148 (m-10) REVERT: A 1834 GLU cc_start: 0.8344 (tt0) cc_final: 0.8072 (tm-30) REVERT: A 1905 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 2115 MET cc_start: 0.4043 (mmm) cc_final: 0.3103 (mmm) REVERT: A 2179 PHE cc_start: 0.7152 (t80) cc_final: 0.6806 (t80) REVERT: A 2318 GLN cc_start: 0.7705 (mm-40) cc_final: 0.6807 (tt0) REVERT: A 2380 MET cc_start: 0.8535 (tpt) cc_final: 0.8263 (tpp) REVERT: A 2449 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5454 (pm20) REVERT: A 2701 THR cc_start: 0.8894 (m) cc_final: 0.8639 (p) REVERT: A 2837 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 2973 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 3047 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8862 (m110) REVERT: A 3073 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: A 3111 GLU cc_start: 0.8172 (tp30) cc_final: 0.7924 (tp30) REVERT: A 3207 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7391 (tpm170) REVERT: A 3265 MET cc_start: 0.6454 (pmm) cc_final: 0.6081 (pmm) REVERT: A 3276 GLU cc_start: 0.8158 (tt0) cc_final: 0.7936 (tt0) REVERT: A 3404 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5394 (mt) REVERT: A 3410 MET cc_start: 0.8345 (mtm) cc_final: 0.7921 (mtt) REVERT: A 3482 GLN cc_start: 0.8943 (mt0) cc_final: 0.8530 (tm-30) REVERT: A 3509 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8844 (mm) REVERT: A 3515 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 3529 MET cc_start: 0.6875 (tpt) cc_final: 0.6478 (mtt) REVERT: A 3553 GLU cc_start: 0.8566 (tp30) cc_final: 0.8263 (tp30) REVERT: A 3556 ASN cc_start: 0.8877 (t0) cc_final: 0.8548 (t0) REVERT: A 3573 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6789 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8270 (mmtt) REVERT: A 3719 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 3819 MET cc_start: 0.8086 (ppp) cc_final: 0.7534 (ppp) REVERT: A 3858 MET cc_start: 0.6561 (pmm) cc_final: 0.6245 (tmm) REVERT: A 4026 MET cc_start: 0.8394 (ptm) cc_final: 0.7877 (ppp) REVERT: A 4029 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8598 (tptt) REVERT: A 4085 LEU cc_start: 0.9209 (tt) cc_final: 0.8877 (pp) REVERT: A 4272 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8054 (mtp-110) REVERT: A 4500 GLN cc_start: 0.4375 (tp-100) cc_final: 0.4015 (mp-120) REVERT: A 4630 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7507 (ptm160) REVERT: A 4688 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.5044 (mmp-170) REVERT: A 4722 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7994 (ttm110) REVERT: A 4729 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: A 4835 ASN cc_start: 0.7644 (t0) cc_final: 0.7012 (m-40) REVERT: A 4901 ARG cc_start: 0.9112 (mmp80) cc_final: 0.8856 (mmp80) REVERT: A 4990 ASN cc_start: 0.9385 (t0) cc_final: 0.9021 (m-40) REVERT: A 5074 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 5107 MET cc_start: 0.6666 (tpt) cc_final: 0.6322 (tpt) REVERT: B 19 MET cc_start: 0.3049 (pmm) cc_final: 0.2065 (pmm) outliers start: 139 outliers final: 61 residues processed: 565 average time/residue: 0.2373 time to fit residues: 220.8829 Evaluate side-chains 476 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 399 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1248 ASN Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1605 VAL Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2044 ILE Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2267 VAL Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2973 VAL Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3047 ASN Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3719 LEU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4607 PHE Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4729 GLU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5074 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 259 optimal weight: 0.8980 chunk 322 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2702 ASN A3047 ASN A3119 GLN A3600 GLN A3653 ASN ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.090211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.074332 restraints weight = 226430.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.075918 restraints weight = 149750.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.077017 restraints weight = 109666.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.077778 restraints weight = 86706.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.078323 restraints weight = 72906.301| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37575 Z= 0.135 Angle : 0.730 14.126 50851 Z= 0.349 Chirality : 0.044 0.274 5723 Planarity : 0.004 0.057 6498 Dihedral : 6.717 135.982 5015 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 3.34 % Allowed : 26.93 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4544 helix: 0.77 (0.10), residues: 2552 sheet: -1.19 (0.34), residues: 233 loop : -2.10 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 646 TYR 0.029 0.001 TYR A4316 PHE 0.025 0.001 PHE A2371 TRP 0.025 0.002 TRP A2181 HIS 0.011 0.001 HIS A4395 Details of bonding type rmsd covalent geometry : bond 0.00300 (37566) covalent geometry : angle 0.72711 (50843) SS BOND : bond 0.00563 ( 1) SS BOND : angle 3.33890 ( 2) hydrogen bonds : bond 0.03500 ( 1857) hydrogen bonds : angle 4.44430 ( 5472) metal coordination : bond 0.00162 ( 7) metal coordination : angle 5.60954 ( 6) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 436 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6443 (mm-30) REVERT: A 795 MET cc_start: 0.5262 (mmp) cc_final: 0.4822 (mmp) REVERT: A 819 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6968 (mm) REVERT: A 969 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7457 (pp20) REVERT: A 1047 ILE cc_start: 0.8636 (mp) cc_final: 0.8071 (tp) REVERT: A 1152 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: A 1189 LEU cc_start: 0.7275 (mp) cc_final: 0.6934 (pp) REVERT: A 1265 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9088 (pp20) REVERT: A 1286 PHE cc_start: 0.8631 (m-80) cc_final: 0.8362 (m-80) REVERT: A 1579 ASN cc_start: 0.8734 (m-40) cc_final: 0.8484 (m-40) REVERT: A 1597 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7461 (pp) REVERT: A 1644 ASP cc_start: 0.8644 (m-30) cc_final: 0.8247 (m-30) REVERT: A 1744 MET cc_start: 0.8746 (mmt) cc_final: 0.8509 (mmt) REVERT: A 1746 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8062 (tp-100) REVERT: A 1810 TYR cc_start: 0.7014 (m-80) cc_final: 0.5902 (m-10) REVERT: A 1905 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 2040 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7828 (p90) REVERT: A 2115 MET cc_start: 0.4226 (mmm) cc_final: 0.3300 (mmm) REVERT: A 2179 PHE cc_start: 0.7165 (t80) cc_final: 0.6748 (t80) REVERT: A 2318 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6667 (tt0) REVERT: A 2380 MET cc_start: 0.8523 (tpt) cc_final: 0.8235 (tpp) REVERT: A 2449 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5354 (pm20) REVERT: A 2585 MET cc_start: 0.8255 (mmt) cc_final: 0.7926 (mmm) REVERT: A 2648 MET cc_start: 0.6496 (mmp) cc_final: 0.6207 (mmp) REVERT: A 2837 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7370 (t80) REVERT: A 2848 TRP cc_start: 0.6964 (OUTLIER) cc_final: 0.6646 (m100) REVERT: A 3073 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: A 3404 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.5074 (mt) REVERT: A 3410 MET cc_start: 0.8311 (mtm) cc_final: 0.7903 (mtt) REVERT: A 3482 GLN cc_start: 0.8730 (mt0) cc_final: 0.8454 (tm-30) REVERT: A 3509 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 3515 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6692 (mm-30) REVERT: A 3573 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6935 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8352 (mmtt) REVERT: A 3707 GLN cc_start: 0.9221 (mt0) cc_final: 0.8714 (mp10) REVERT: A 3727 ARG cc_start: 0.7809 (mpp-170) cc_final: 0.7335 (mpp-170) REVERT: A 3728 GLU cc_start: 0.8571 (mp0) cc_final: 0.8148 (mp0) REVERT: A 3774 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7966 (mtm180) REVERT: A 3819 MET cc_start: 0.8121 (ppp) cc_final: 0.7547 (ppp) REVERT: A 4026 MET cc_start: 0.8219 (ptm) cc_final: 0.7776 (ppp) REVERT: A 4029 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8498 (tptt) REVERT: A 4500 GLN cc_start: 0.4501 (tp-100) cc_final: 0.4134 (mp-120) REVERT: A 4688 ARG cc_start: 0.5855 (OUTLIER) cc_final: 0.5118 (mmp-170) REVERT: A 4737 LEU cc_start: 0.8553 (tp) cc_final: 0.8281 (tp) REVERT: A 4835 ASN cc_start: 0.7457 (t0) cc_final: 0.6870 (m-40) REVERT: A 4860 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7288 (p0) REVERT: A 4901 ARG cc_start: 0.9167 (mmp80) cc_final: 0.8919 (mmp80) REVERT: A 5074 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8949 (mm) REVERT: A 5107 MET cc_start: 0.6069 (tpt) cc_final: 0.5815 (tpt) REVERT: A 5128 MET cc_start: 0.6161 (tpp) cc_final: 0.5786 (tpp) REVERT: B 19 MET cc_start: 0.3471 (pmm) cc_final: 0.1833 (mmm) REVERT: B 131 LYS cc_start: 0.7117 (mmtm) cc_final: 0.6810 (pttp) outliers start: 137 outliers final: 78 residues processed: 546 average time/residue: 0.2213 time to fit residues: 199.7358 Evaluate side-chains 490 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 396 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1520 ILE Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2040 TYR Chi-restraints excluded: chain A residue 2044 ILE Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2267 VAL Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2391 ILE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2848 TRP Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3092 LEU Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3183 ASP Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4419 VAL Chi-restraints excluded: chain A residue 4529 THR Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4607 PHE Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4676 SER Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain B residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 261 optimal weight: 8.9990 chunk 287 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 453 optimal weight: 0.0170 chunk 123 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS A1129 GLN ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2186 GLN A2288 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4759 HIS ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.091415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.074957 restraints weight = 223054.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.076671 restraints weight = 144158.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.077766 restraints weight = 103652.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.078520 restraints weight = 82188.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.079066 restraints weight = 69424.823| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37575 Z= 0.173 Angle : 0.769 22.251 50851 Z= 0.368 Chirality : 0.044 0.218 5723 Planarity : 0.005 0.084 6498 Dihedral : 6.791 138.780 5013 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.47 % Rotamer: Outliers : 3.80 % Allowed : 26.64 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4544 helix: 0.71 (0.10), residues: 2564 sheet: -1.01 (0.34), residues: 236 loop : -2.10 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A4722 TYR 0.030 0.002 TYR A4316 PHE 0.031 0.002 PHE A3778 TRP 0.039 0.002 TRP A2346 HIS 0.010 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00382 (37566) covalent geometry : angle 0.76678 (50843) SS BOND : bond 0.00294 ( 1) SS BOND : angle 1.74203 ( 2) hydrogen bonds : bond 0.03615 ( 1857) hydrogen bonds : angle 4.50673 ( 5472) metal coordination : bond 0.00177 ( 7) metal coordination : angle 5.23180 ( 6) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 423 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.6713 (mmm) cc_final: 0.6465 (mmt) REVERT: A 644 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5917 (mtt180) REVERT: A 748 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 792 LYS cc_start: 0.9055 (pttt) cc_final: 0.8818 (ptmt) REVERT: A 795 MET cc_start: 0.5276 (mmp) cc_final: 0.4874 (mmp) REVERT: A 819 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6784 (mm) REVERT: A 969 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7257 (pp20) REVERT: A 1026 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8906 (tptt) REVERT: A 1047 ILE cc_start: 0.8803 (mp) cc_final: 0.8298 (tp) REVERT: A 1152 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: A 1265 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9123 (pp20) REVERT: A 1286 PHE cc_start: 0.8823 (m-80) cc_final: 0.8477 (m-80) REVERT: A 1551 LEU cc_start: 0.8779 (pp) cc_final: 0.8209 (tp) REVERT: A 1579 ASN cc_start: 0.8712 (m-40) cc_final: 0.8475 (m-40) REVERT: A 1644 ASP cc_start: 0.8708 (m-30) cc_final: 0.8310 (m-30) REVERT: A 1689 MET cc_start: 0.7541 (mmp) cc_final: 0.6649 (ttt) REVERT: A 1746 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8043 (tp-100) REVERT: A 1810 TYR cc_start: 0.7150 (m-80) cc_final: 0.6028 (m-10) REVERT: A 1825 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6678 (tp) REVERT: A 1905 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: A 2115 MET cc_start: 0.4833 (mmm) cc_final: 0.3817 (mmm) REVERT: A 2179 PHE cc_start: 0.7076 (t80) cc_final: 0.6620 (t80) REVERT: A 2307 MET cc_start: 0.3466 (pmm) cc_final: 0.3074 (pmm) REVERT: A 2318 GLN cc_start: 0.7644 (mm-40) cc_final: 0.6800 (tt0) REVERT: A 2380 MET cc_start: 0.8801 (tpt) cc_final: 0.8410 (tpp) REVERT: A 2449 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5612 (pm20) REVERT: A 2587 MET cc_start: 0.8342 (mmt) cc_final: 0.8125 (ttt) REVERT: A 2837 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 3073 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: A 3265 MET cc_start: 0.6347 (pmm) cc_final: 0.6056 (pmm) REVERT: A 3276 GLU cc_start: 0.8106 (tt0) cc_final: 0.7856 (tt0) REVERT: A 3404 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5552 (mt) REVERT: A 3410 MET cc_start: 0.8303 (mtm) cc_final: 0.7925 (mtt) REVERT: A 3482 GLN cc_start: 0.8795 (mt0) cc_final: 0.8470 (tm-30) REVERT: A 3491 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.4009 (ppp) REVERT: A 3509 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8772 (mm) REVERT: A 3515 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6878 (tp30) REVERT: A 3553 GLU cc_start: 0.8490 (tp30) cc_final: 0.8089 (tp30) REVERT: A 3573 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6803 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8477 (mmtt) REVERT: A 3727 ARG cc_start: 0.7896 (mpp-170) cc_final: 0.7626 (mpp-170) REVERT: A 3774 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8006 (mtm180) REVERT: A 3806 MET cc_start: 0.8297 (tmm) cc_final: 0.7602 (tmm) REVERT: A 3819 MET cc_start: 0.8354 (ppp) cc_final: 0.7794 (ppp) REVERT: A 3858 MET cc_start: 0.7538 (tmm) cc_final: 0.6201 (pmm) REVERT: A 4026 MET cc_start: 0.8350 (ptm) cc_final: 0.7827 (ppp) REVERT: A 4029 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8580 (tptt) REVERT: A 4238 MET cc_start: 0.7656 (tmm) cc_final: 0.7237 (tmm) REVERT: A 4269 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7029 (pp) REVERT: A 4392 MET cc_start: 0.8825 (mpp) cc_final: 0.8276 (mmm) REVERT: A 4500 GLN cc_start: 0.4323 (tp-100) cc_final: 0.3911 (mp-120) REVERT: A 4688 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.4919 (mmp-170) REVERT: A 4860 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7500 (p0) REVERT: A 4927 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7689 (t0) REVERT: A 4972 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7721 (pp20) REVERT: A 5074 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 5078 GLU cc_start: 0.7624 (pt0) cc_final: 0.7246 (pt0) REVERT: A 5126 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7255 (mm) REVERT: B 19 MET cc_start: 0.3572 (pmm) cc_final: 0.2015 (mmm) outliers start: 156 outliers final: 98 residues processed: 546 average time/residue: 0.2321 time to fit residues: 209.7465 Evaluate side-chains 513 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 397 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1451 PHE Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1520 ILE Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2044 ILE Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2634 THR Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain A residue 2743 VAL Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2851 ASP Chi-restraints excluded: chain A residue 2889 ILE Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3183 ASP Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3491 MET Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3772 ARG Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4102 ASN Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4419 VAL Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4642 ILE Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4712 TRP Chi-restraints excluded: chain A residue 4713 HIS Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4752 ILE Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 4822 CYS Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 4927 ASP Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain A residue 5126 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 434 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 419 optimal weight: 7.9990 chunk 433 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 400 optimal weight: 5.9990 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 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1849 GLN ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2360 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3532 HIS A3538 GLN A3542 GLN ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS A4133 HIS ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4600 GLN A4879 ASN ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4900 GLN ** A4932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.086273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.070381 restraints weight = 232373.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.071896 restraints weight = 153660.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.072946 restraints weight = 113412.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.073602 restraints weight = 90108.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.074165 restraints weight = 76653.496| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37575 Z= 0.174 Angle : 0.773 16.222 50851 Z= 0.371 Chirality : 0.044 0.236 5723 Planarity : 0.004 0.085 6498 Dihedral : 6.715 136.523 5013 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 3.85 % Allowed : 26.88 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 4544 helix: 0.65 (0.10), residues: 2562 sheet: -1.11 (0.34), residues: 226 loop : -2.10 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A4722 TYR 0.024 0.002 TYR A4316 PHE 0.027 0.002 PHE A2371 TRP 0.046 0.002 TRP A2346 HIS 0.013 0.001 HIS A4395 Details of bonding type rmsd covalent geometry : bond 0.00387 (37566) covalent geometry : angle 0.77173 (50843) SS BOND : bond 0.00225 ( 1) SS BOND : angle 1.69513 ( 2) hydrogen bonds : bond 0.03664 ( 1857) hydrogen bonds : angle 4.55293 ( 5472) metal coordination : bond 0.00261 ( 7) metal coordination : angle 4.79397 ( 6) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 417 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 ARG cc_start: 0.6177 (mtt180) cc_final: 0.5938 (mtt180) REVERT: A 748 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 792 LYS cc_start: 0.9019 (pttt) cc_final: 0.8807 (ptmt) REVERT: A 795 MET cc_start: 0.5344 (mmp) cc_final: 0.4891 (mmp) REVERT: A 819 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6892 (mm) REVERT: A 969 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7069 (pp20) REVERT: A 1026 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8839 (tptt) REVERT: A 1152 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: A 1189 LEU cc_start: 0.6430 (mp) cc_final: 0.6149 (pp) REVERT: A 1255 ASN cc_start: 0.9278 (t0) cc_final: 0.8929 (t0) REVERT: A 1286 PHE cc_start: 0.8631 (m-80) cc_final: 0.8267 (m-80) REVERT: A 1579 ASN cc_start: 0.8788 (m-40) cc_final: 0.8552 (m-40) REVERT: A 1644 ASP cc_start: 0.8768 (m-30) cc_final: 0.8309 (m-30) REVERT: A 1689 MET cc_start: 0.7588 (mmp) cc_final: 0.6651 (ttt) REVERT: A 1746 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8255 (tp-100) REVERT: A 1905 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: A 2115 MET cc_start: 0.5244 (mmm) cc_final: 0.3890 (mmm) REVERT: A 2179 PHE cc_start: 0.7283 (t80) cc_final: 0.6787 (t80) REVERT: A 2307 MET cc_start: 0.3358 (pmm) cc_final: 0.2597 (pmm) REVERT: A 2318 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6747 (tt0) REVERT: A 2380 MET cc_start: 0.8697 (tpt) cc_final: 0.8348 (tpp) REVERT: A 2449 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5728 (pm20) REVERT: A 2587 MET cc_start: 0.8464 (mmt) cc_final: 0.8106 (ttt) REVERT: A 2648 MET cc_start: 0.6445 (mmp) cc_final: 0.6184 (mmp) REVERT: A 2702 ASN cc_start: 0.7957 (m-40) cc_final: 0.7606 (m-40) REVERT: A 2925 PHE cc_start: 0.7761 (t80) cc_final: 0.7366 (t80) REVERT: A 3207 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7541 (tpm170) REVERT: A 3265 MET cc_start: 0.6607 (pmm) cc_final: 0.6145 (pmm) REVERT: A 3404 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5518 (mt) REVERT: A 3410 MET cc_start: 0.8121 (mtm) cc_final: 0.7695 (mtm) REVERT: A 3482 GLN cc_start: 0.8845 (mt0) cc_final: 0.8530 (tm-30) REVERT: A 3491 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.3756 (ppp) REVERT: A 3509 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 3515 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6558 (tp30) REVERT: A 3538 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6993 (tp-100) REVERT: A 3573 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6975 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8663 (mmtt) REVERT: A 3714 LEU cc_start: 0.8968 (tp) cc_final: 0.8649 (mm) REVERT: A 3735 MET cc_start: 0.8880 (ppp) cc_final: 0.8633 (ppp) REVERT: A 3774 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8011 (mtm180) REVERT: A 3806 MET cc_start: 0.8437 (tmm) cc_final: 0.7969 (tmm) REVERT: A 3819 MET cc_start: 0.8468 (ppp) cc_final: 0.7982 (ppp) REVERT: A 4026 MET cc_start: 0.8189 (ptm) cc_final: 0.7693 (ppp) REVERT: A 4029 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8614 (tptt) REVERT: A 4085 LEU cc_start: 0.9070 (tt) cc_final: 0.8716 (pp) REVERT: A 4238 MET cc_start: 0.7887 (tmm) cc_final: 0.7470 (tmm) REVERT: A 4269 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7317 (pp) REVERT: A 4500 GLN cc_start: 0.4552 (tp-100) cc_final: 0.4030 (mp-120) REVERT: A 4688 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.4996 (mmp-170) REVERT: A 4717 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8742 (mmtm) REVERT: A 4860 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7782 (p0) REVERT: A 4861 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8494 (pp) REVERT: A 4875 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8442 (pp) REVERT: A 4879 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6939 (p0) REVERT: A 4901 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8607 (mmp80) REVERT: A 4927 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7705 (t0) REVERT: A 4972 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7624 (pp20) REVERT: A 5074 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 5078 GLU cc_start: 0.7710 (pt0) cc_final: 0.7314 (pt0) REVERT: A 5107 MET cc_start: 0.7284 (ptp) cc_final: 0.6715 (tpt) REVERT: B 19 MET cc_start: 0.3965 (pmm) cc_final: 0.2483 (mmm) REVERT: B 63 PHE cc_start: 0.8892 (m-80) cc_final: 0.8690 (m-10) REVERT: B 131 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6694 (pttp) outliers start: 158 outliers final: 107 residues processed: 542 average time/residue: 0.2453 time to fit residues: 217.9958 Evaluate side-chains 514 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 389 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1771 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2037 ILE Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2449 GLU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2634 THR Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2743 VAL Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2820 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2889 ILE Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3183 ASP Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3274 PHE Chi-restraints excluded: chain A residue 3275 THR Chi-restraints excluded: chain A residue 3278 THR Chi-restraints excluded: chain A residue 3291 VAL Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3491 MET Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3538 GLN Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3578 VAL Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3772 ARG Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3779 SER Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3841 THR Chi-restraints excluded: chain A residue 3859 THR Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4001 HIS Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4102 ASN Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4319 LEU Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4419 VAL Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4577 MET Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4642 ILE Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4695 LEU Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4713 HIS Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4752 ILE Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 4822 CYS Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 4861 LEU Chi-restraints excluded: chain A residue 4875 LEU Chi-restraints excluded: chain A residue 4879 ASN Chi-restraints excluded: chain A residue 4927 ASP Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain B residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 156 optimal weight: 0.0270 chunk 189 optimal weight: 0.0970 chunk 231 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 455 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 371 optimal weight: 0.0970 chunk 353 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2360 ASN ** A2584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 ASN ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS A4133 HIS ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.089009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.073362 restraints weight = 224256.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.074924 restraints weight = 147487.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.075989 restraints weight = 108050.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.076747 restraints weight = 85446.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.077198 restraints weight = 71545.914| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37575 Z= 0.129 Angle : 0.767 17.304 50851 Z= 0.362 Chirality : 0.044 0.242 5723 Planarity : 0.004 0.086 6498 Dihedral : 6.514 134.911 5013 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 2.66 % Allowed : 28.52 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4544 helix: 0.72 (0.10), residues: 2562 sheet: -1.03 (0.35), residues: 237 loop : -2.03 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3780 TYR 0.023 0.001 TYR A4316 PHE 0.047 0.001 PHE A1126 TRP 0.050 0.002 TRP A2346 HIS 0.021 0.001 HIS A4001 Details of bonding type rmsd covalent geometry : bond 0.00280 (37566) covalent geometry : angle 0.76559 (50843) SS BOND : bond 0.00310 ( 1) SS BOND : angle 1.27282 ( 2) hydrogen bonds : bond 0.03455 ( 1857) hydrogen bonds : angle 4.41452 ( 5472) metal coordination : bond 0.00203 ( 7) metal coordination : angle 4.34261 ( 6) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 425 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 795 MET cc_start: 0.5202 (mmp) cc_final: 0.4780 (mmp) REVERT: A 969 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7002 (pp20) REVERT: A 1152 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: A 1189 LEU cc_start: 0.6657 (mp) cc_final: 0.6336 (pp) REVERT: A 1204 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6131 (mmmt) REVERT: A 1255 ASN cc_start: 0.9254 (t0) cc_final: 0.8875 (t0) REVERT: A 1286 PHE cc_start: 0.8574 (m-80) cc_final: 0.8336 (m-80) REVERT: A 1644 ASP cc_start: 0.8649 (m-30) cc_final: 0.8230 (m-30) REVERT: A 1689 MET cc_start: 0.7471 (mmp) cc_final: 0.6595 (ttt) REVERT: A 1746 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7982 (tp-100) REVERT: A 1825 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6641 (tp) REVERT: A 1905 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: A 2022 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 2115 MET cc_start: 0.5123 (mmm) cc_final: 0.3856 (mmm) REVERT: A 2129 TYR cc_start: 0.0304 (OUTLIER) cc_final: -0.0947 (t80) REVERT: A 2276 MET cc_start: 0.8873 (mtm) cc_final: 0.8489 (mtt) REVERT: A 2303 LYS cc_start: 0.6144 (pptt) cc_final: 0.5910 (pptt) REVERT: A 2318 GLN cc_start: 0.7531 (mm-40) cc_final: 0.6659 (tt0) REVERT: A 2380 MET cc_start: 0.8688 (tpt) cc_final: 0.8154 (tpp) REVERT: A 2585 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: A 2587 MET cc_start: 0.8293 (mmt) cc_final: 0.7893 (ttt) REVERT: A 2648 MET cc_start: 0.6318 (mmp) cc_final: 0.6048 (mmp) REVERT: A 2660 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: A 2702 ASN cc_start: 0.7976 (m-40) cc_final: 0.7515 (m-40) REVERT: A 2837 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7330 (t80) REVERT: A 2925 PHE cc_start: 0.7665 (t80) cc_final: 0.7169 (t80) REVERT: A 3073 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: A 3115 VAL cc_start: 0.8866 (m) cc_final: 0.8416 (p) REVERT: A 3170 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5295 (tptp) REVERT: A 3265 MET cc_start: 0.6600 (pmm) cc_final: 0.6308 (pmm) REVERT: A 3404 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5371 (mt) REVERT: A 3482 GLN cc_start: 0.8714 (mt0) cc_final: 0.8504 (tm-30) REVERT: A 3548 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7105 (pm20) REVERT: A 3573 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6813 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8885 (ttpp) cc_final: 0.8615 (mmtt) REVERT: A 3774 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8066 (ptm160) REVERT: A 3780 ARG cc_start: 0.9008 (ttp-110) cc_final: 0.8683 (mtt180) REVERT: A 3806 MET cc_start: 0.8201 (tmm) cc_final: 0.7939 (tmm) REVERT: A 3819 MET cc_start: 0.8427 (ppp) cc_final: 0.7951 (ppp) REVERT: A 3858 MET cc_start: 0.7441 (tmm) cc_final: 0.6098 (pmm) REVERT: A 3919 ARG cc_start: 0.9119 (tpm170) cc_final: 0.8888 (tpm170) REVERT: A 4026 MET cc_start: 0.8042 (ptm) cc_final: 0.7543 (ppp) REVERT: A 4029 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8505 (tptt) REVERT: A 4085 LEU cc_start: 0.9085 (tt) cc_final: 0.8765 (pp) REVERT: A 4238 MET cc_start: 0.7920 (tmm) cc_final: 0.7518 (tmm) REVERT: A 4269 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7107 (pp) REVERT: A 4392 MET cc_start: 0.8840 (mpp) cc_final: 0.8196 (mmm) REVERT: A 4688 ARG cc_start: 0.5816 (OUTLIER) cc_final: 0.5065 (mmp-170) REVERT: A 4717 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8660 (mmtm) REVERT: A 4860 ASP cc_start: 0.7940 (m-30) cc_final: 0.7605 (p0) REVERT: A 4901 ARG cc_start: 0.8906 (mmp80) cc_final: 0.8527 (mmp80) REVERT: A 4972 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7630 (pp20) REVERT: A 5010 PHE cc_start: 0.8302 (m-10) cc_final: 0.8101 (m-80) REVERT: A 5078 GLU cc_start: 0.7650 (pt0) cc_final: 0.7224 (pt0) REVERT: A 5107 MET cc_start: 0.7023 (ptp) cc_final: 0.6715 (tpt) REVERT: A 5128 MET cc_start: 0.6089 (tpp) cc_final: 0.5830 (tpp) REVERT: B 19 MET cc_start: 0.3837 (pmm) cc_final: 0.2358 (mmm) REVERT: B 131 LYS cc_start: 0.7160 (mmtm) cc_final: 0.6675 (pttp) outliers start: 109 outliers final: 67 residues processed: 517 average time/residue: 0.2280 time to fit residues: 194.0526 Evaluate side-chains 472 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 389 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1204 LYS Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1905 PHE Chi-restraints excluded: chain A residue 1958 VAL Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2129 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2660 GLU Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2820 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3073 ASP Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3170 LYS Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3274 PHE Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4133 HIS Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4642 ILE Chi-restraints excluded: chain A residue 4676 SER Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4713 HIS Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4752 ILE Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain B residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 49 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 378 optimal weight: 0.0060 chunk 319 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 418 optimal weight: 20.0000 chunk 236 optimal weight: 0.0870 chunk 396 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2360 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2584 GLN ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3041 GLN A3045 ASN ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4133 HIS ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 GLN A5056 HIS A5094 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.089896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.073353 restraints weight = 223115.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.075003 restraints weight = 147071.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.076112 restraints weight = 105970.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.076881 restraints weight = 83918.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.077425 restraints weight = 70691.325| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37575 Z= 0.165 Angle : 0.777 16.099 50851 Z= 0.374 Chirality : 0.044 0.285 5723 Planarity : 0.004 0.078 6498 Dihedral : 6.487 135.338 5010 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 2.85 % Allowed : 28.42 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4544 helix: 0.72 (0.10), residues: 2560 sheet: -0.92 (0.36), residues: 217 loop : -1.98 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 892 TYR 0.021 0.002 TYR A4316 PHE 0.036 0.002 PHE A1126 TRP 0.054 0.002 TRP A2346 HIS 0.011 0.001 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00365 (37566) covalent geometry : angle 0.77574 (50843) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.22450 ( 2) hydrogen bonds : bond 0.03605 ( 1857) hydrogen bonds : angle 4.53286 ( 5472) metal coordination : bond 0.00307 ( 7) metal coordination : angle 3.93996 ( 6) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 385 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.6551 (mmm) cc_final: 0.6349 (mmm) REVERT: A 748 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 795 MET cc_start: 0.5349 (mmp) cc_final: 0.4893 (mmp) REVERT: A 969 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7011 (pp20) REVERT: A 1152 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: A 1189 LEU cc_start: 0.6748 (mp) cc_final: 0.6428 (pp) REVERT: A 1196 MET cc_start: 0.7266 (ppp) cc_final: 0.6912 (ppp) REVERT: A 1255 ASN cc_start: 0.9310 (t0) cc_final: 0.8997 (t0) REVERT: A 1644 ASP cc_start: 0.8637 (m-30) cc_final: 0.8296 (m-30) REVERT: A 1690 MET cc_start: 0.5352 (ttt) cc_final: 0.5013 (ttt) REVERT: A 1746 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8075 (tp-100) REVERT: A 2115 MET cc_start: 0.5502 (mmm) cc_final: 0.4551 (mmm) REVERT: A 2307 MET cc_start: 0.3876 (pmm) cc_final: 0.3100 (pmm) REVERT: A 2318 GLN cc_start: 0.7608 (mm-40) cc_final: 0.6822 (tt0) REVERT: A 2380 MET cc_start: 0.8624 (tpt) cc_final: 0.8097 (tpp) REVERT: A 2585 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: A 2587 MET cc_start: 0.8332 (mmt) cc_final: 0.8076 (ttt) REVERT: A 2702 ASN cc_start: 0.8176 (m-40) cc_final: 0.7532 (m-40) REVERT: A 2715 MET cc_start: 0.8380 (ppp) cc_final: 0.8005 (ppp) REVERT: A 2925 PHE cc_start: 0.7869 (t80) cc_final: 0.7400 (t80) REVERT: A 3111 GLU cc_start: 0.8034 (tp30) cc_final: 0.7799 (tp30) REVERT: A 3115 VAL cc_start: 0.8860 (m) cc_final: 0.8351 (p) REVERT: A 3265 MET cc_start: 0.6848 (pmm) cc_final: 0.6398 (pmm) REVERT: A 3404 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5615 (mt) REVERT: A 3482 GLN cc_start: 0.8795 (mt0) cc_final: 0.8543 (tm-30) REVERT: A 3553 GLU cc_start: 0.8419 (tp30) cc_final: 0.8168 (tp30) REVERT: A 3573 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6923 (tpp-160) REVERT: A 3683 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8689 (mmtt) REVERT: A 3714 LEU cc_start: 0.8935 (tp) cc_final: 0.8621 (mm) REVERT: A 3774 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7998 (mtm180) REVERT: A 3806 MET cc_start: 0.8397 (tmm) cc_final: 0.8066 (tmm) REVERT: A 3819 MET cc_start: 0.8500 (ppp) cc_final: 0.8022 (ppp) REVERT: A 3919 ARG cc_start: 0.9202 (tpm170) cc_final: 0.8949 (tpm170) REVERT: A 4026 MET cc_start: 0.8236 (ptm) cc_final: 0.7594 (ppp) REVERT: A 4029 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8620 (tptt) REVERT: A 4085 LEU cc_start: 0.9110 (tt) cc_final: 0.8718 (pp) REVERT: A 4238 MET cc_start: 0.7987 (tmm) cc_final: 0.7608 (tmm) REVERT: A 4269 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7263 (pp) REVERT: A 4392 MET cc_start: 0.8826 (mpp) cc_final: 0.8210 (mmm) REVERT: A 4688 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.4884 (mmp-170) REVERT: A 4717 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8824 (mmtm) REVERT: A 4782 LEU cc_start: 0.9092 (tp) cc_final: 0.8791 (pp) REVERT: A 4860 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7985 (p0) REVERT: A 4861 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 4875 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8532 (pp) REVERT: A 5074 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8924 (mm) REVERT: A 5078 GLU cc_start: 0.7761 (pt0) cc_final: 0.7344 (pt0) REVERT: A 5107 MET cc_start: 0.7157 (ptp) cc_final: 0.6546 (tpt) REVERT: B 19 MET cc_start: 0.4009 (pmm) cc_final: 0.2281 (mmm) REVERT: B 131 LYS cc_start: 0.7373 (mmtm) cc_final: 0.6772 (pttp) outliers start: 117 outliers final: 86 residues processed: 478 average time/residue: 0.2287 time to fit residues: 180.8150 Evaluate side-chains 476 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 379 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1553 ASN Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2022 THR Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2256 ARG Chi-restraints excluded: chain A residue 2302 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2585 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2709 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2820 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3274 PHE Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3582 LEU Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3859 THR Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4102 ASN Chi-restraints excluded: chain A residue 4133 HIS Chi-restraints excluded: chain A residue 4269 LEU Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4642 ILE Chi-restraints excluded: chain A residue 4676 SER Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4707 THR Chi-restraints excluded: chain A residue 4713 HIS Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4752 ILE Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 4860 ASP Chi-restraints excluded: chain A residue 4861 LEU Chi-restraints excluded: chain A residue 4875 LEU Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5074 LEU Chi-restraints excluded: chain B residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 116 optimal weight: 5.9990 chunk 413 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 354 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 345 optimal weight: 0.7980 chunk 447 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2360 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4371 ASN ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.083701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.067773 restraints weight = 233594.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.069218 restraints weight = 155051.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.070223 restraints weight = 114781.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.070848 restraints weight = 91794.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.071363 restraints weight = 78733.095| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37575 Z= 0.211 Angle : 0.825 16.958 50851 Z= 0.402 Chirality : 0.046 0.322 5723 Planarity : 0.005 0.084 6498 Dihedral : 6.634 137.919 5010 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.34 % Favored : 91.62 % Rotamer: Outliers : 2.90 % Allowed : 28.27 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4544 helix: 0.53 (0.10), residues: 2557 sheet: -1.14 (0.35), residues: 218 loop : -2.03 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 642 TYR 0.022 0.002 TYR A4316 PHE 0.039 0.002 PHE A1905 TRP 0.060 0.002 TRP A2346 HIS 0.021 0.002 HIS A4133 Details of bonding type rmsd covalent geometry : bond 0.00461 (37566) covalent geometry : angle 0.82338 (50843) SS BOND : bond 0.00393 ( 1) SS BOND : angle 1.39203 ( 2) hydrogen bonds : bond 0.03846 ( 1857) hydrogen bonds : angle 4.69957 ( 5472) metal coordination : bond 0.00239 ( 7) metal coordination : angle 4.35529 ( 6) Misc. bond : bond 0.00022 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9088 Ramachandran restraints generated. 4544 Oldfield, 0 Emsley, 4544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 390 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.6443 (mmm) cc_final: 0.6215 (mmm) REVERT: A 748 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6829 (mm-30) REVERT: A 795 MET cc_start: 0.5435 (mmp) cc_final: 0.4996 (mmp) REVERT: A 969 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7191 (pp20) REVERT: A 1026 LYS cc_start: 0.9384 (mmmt) cc_final: 0.9157 (mttt) REVERT: A 1152 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: A 1196 MET cc_start: 0.7394 (ppp) cc_final: 0.7132 (ppp) REVERT: A 1204 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6432 (mmmt) REVERT: A 1255 ASN cc_start: 0.9301 (t0) cc_final: 0.8982 (t0) REVERT: A 1442 MET cc_start: 0.2937 (mmt) cc_final: 0.2622 (mmt) REVERT: A 1644 ASP cc_start: 0.8775 (m-30) cc_final: 0.8410 (m-30) REVERT: A 1689 MET cc_start: 0.7632 (mmp) cc_final: 0.6816 (ttt) REVERT: A 1744 MET cc_start: 0.8290 (tpt) cc_final: 0.8029 (tpt) REVERT: A 1746 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8341 (tp-100) REVERT: A 2115 MET cc_start: 0.5869 (mmm) cc_final: 0.5072 (mmm) REVERT: A 2129 TYR cc_start: 0.0557 (OUTLIER) cc_final: -0.0680 (t80) REVERT: A 2307 MET cc_start: 0.4185 (pmm) cc_final: 0.3477 (pmm) REVERT: A 2318 GLN cc_start: 0.7695 (mm-40) cc_final: 0.6985 (tt0) REVERT: A 2380 MET cc_start: 0.8830 (tpt) cc_final: 0.8264 (tpp) REVERT: A 2500 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: A 2585 MET cc_start: 0.8538 (mmt) cc_final: 0.8002 (mmm) REVERT: A 2587 MET cc_start: 0.8600 (mmt) cc_final: 0.8381 (ttt) REVERT: A 2648 MET cc_start: 0.6736 (mmp) cc_final: 0.6481 (mmp) REVERT: A 2925 PHE cc_start: 0.7837 (t80) cc_final: 0.7527 (t80) REVERT: A 3404 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5717 (mt) REVERT: A 3482 GLN cc_start: 0.8800 (mt0) cc_final: 0.8514 (tm-30) REVERT: A 3553 GLU cc_start: 0.8343 (tp30) cc_final: 0.8104 (tp30) REVERT: A 3573 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6903 (tpp-160) REVERT: A 3683 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8752 (mmtt) REVERT: A 3714 LEU cc_start: 0.8929 (tp) cc_final: 0.8626 (mm) REVERT: A 3774 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7689 (mtm180) REVERT: A 3780 ARG cc_start: 0.9053 (ttp-110) cc_final: 0.8715 (ttt180) REVERT: A 3806 MET cc_start: 0.8223 (tmm) cc_final: 0.6893 (tmm) REVERT: A 3819 MET cc_start: 0.8536 (ppp) cc_final: 0.8075 (ppp) REVERT: A 3919 ARG cc_start: 0.9153 (tpm170) cc_final: 0.8900 (tpm170) REVERT: A 4026 MET cc_start: 0.8153 (ptm) cc_final: 0.7532 (ppp) REVERT: A 4029 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8637 (tptt) REVERT: A 4085 LEU cc_start: 0.9100 (tt) cc_final: 0.8688 (pp) REVERT: A 4238 MET cc_start: 0.8038 (tmm) cc_final: 0.7329 (tmm) REVERT: A 4272 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.7651 (tpp-160) REVERT: A 4391 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9055 (mt-10) REVERT: A 4392 MET cc_start: 0.8830 (mpp) cc_final: 0.8390 (mmt) REVERT: A 4688 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5170 (mmp-170) REVERT: A 4717 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8783 (mmtm) REVERT: A 4837 MET cc_start: 0.7599 (ppp) cc_final: 0.6715 (ppp) REVERT: A 4861 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8635 (pp) REVERT: A 4875 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8522 (pp) REVERT: A 4972 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7645 (pp20) REVERT: A 5012 ARG cc_start: 0.8542 (ttm170) cc_final: 0.8275 (ttm170) REVERT: A 5078 GLU cc_start: 0.7707 (pt0) cc_final: 0.7299 (pt0) REVERT: A 5107 MET cc_start: 0.7376 (ptp) cc_final: 0.6856 (tpt) REVERT: B 19 MET cc_start: 0.4001 (pmm) cc_final: 0.2470 (mmm) outliers start: 119 outliers final: 92 residues processed: 484 average time/residue: 0.2122 time to fit residues: 169.1019 Evaluate side-chains 469 residues out of total 4115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1152 PHE Chi-restraints excluded: chain A residue 1380 CYS Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1451 PHE Chi-restraints excluded: chain A residue 1520 ILE Chi-restraints excluded: chain A residue 1545 THR Chi-restraints excluded: chain A residue 1553 ASN Chi-restraints excluded: chain A residue 1602 THR Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1764 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1901 ILE Chi-restraints excluded: chain A residue 1941 VAL Chi-restraints excluded: chain A residue 1947 CYS Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2026 THR Chi-restraints excluded: chain A residue 2129 TYR Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2256 ARG Chi-restraints excluded: chain A residue 2302 ILE Chi-restraints excluded: chain A residue 2340 LEU Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2500 GLU Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2573 THR Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 2619 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2630 SER Chi-restraints excluded: chain A residue 2652 VAL Chi-restraints excluded: chain A residue 2679 SER Chi-restraints excluded: chain A residue 2709 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2837 TYR Chi-restraints excluded: chain A residue 2889 ILE Chi-restraints excluded: chain A residue 2942 HIS Chi-restraints excluded: chain A residue 2976 VAL Chi-restraints excluded: chain A residue 3014 ILE Chi-restraints excluded: chain A residue 3031 SER Chi-restraints excluded: chain A residue 3135 MET Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3146 ILE Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3274 PHE Chi-restraints excluded: chain A residue 3292 LEU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3404 LEU Chi-restraints excluded: chain A residue 3562 GLU Chi-restraints excluded: chain A residue 3565 THR Chi-restraints excluded: chain A residue 3573 ARG Chi-restraints excluded: chain A residue 3643 SER Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3764 VAL Chi-restraints excluded: chain A residue 3772 ARG Chi-restraints excluded: chain A residue 3774 ARG Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3835 LEU Chi-restraints excluded: chain A residue 3859 THR Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4102 ASN Chi-restraints excluded: chain A residue 4312 GLN Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4364 PHE Chi-restraints excluded: chain A residue 4566 HIS Chi-restraints excluded: chain A residue 4618 ASN Chi-restraints excluded: chain A residue 4627 LEU Chi-restraints excluded: chain A residue 4642 ILE Chi-restraints excluded: chain A residue 4688 ARG Chi-restraints excluded: chain A residue 4713 HIS Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4752 ILE Chi-restraints excluded: chain A residue 4792 ILE Chi-restraints excluded: chain A residue 4811 VAL Chi-restraints excluded: chain A residue 4822 CYS Chi-restraints excluded: chain A residue 4861 LEU Chi-restraints excluded: chain A residue 4875 LEU Chi-restraints excluded: chain A residue 5034 LEU Chi-restraints excluded: chain A residue 5040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 186 optimal weight: 0.0470 chunk 439 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 79 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 393 optimal weight: 0.3980 chunk 302 optimal weight: 0.2980 chunk 454 optimal weight: 20.0000 chunk 276 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2360 ASN ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.083971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.068343 restraints weight = 238785.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.069792 restraints weight = 158624.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.070767 restraints weight = 117065.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.071393 restraints weight = 94048.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.071898 restraints weight = 80160.953| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 37575 Z= 0.266 Angle : 0.930 59.198 50851 Z= 0.474 Chirality : 0.048 1.089 5723 Planarity : 0.005 0.092 6498 Dihedral : 6.603 137.928 5008 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 2.66 % Allowed : 28.91 % Favored : 68.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4544 helix: 0.54 (0.10), residues: 2554 sheet: -1.15 (0.35), residues: 218 loop : -2.04 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.001 ARG A3271 TYR 0.021 0.002 TYR A4316 PHE 0.141 0.003 PHE A2162 TRP 0.054 0.002 TRP A2346 HIS 0.015 0.002 HIS A2474 Details of bonding type rmsd covalent geometry : bond 0.00608 (37566) covalent geometry : angle 0.92845 (50843) SS BOND : bond 0.00533 ( 1) SS BOND : angle 1.48156 ( 2) hydrogen bonds : bond 0.03856 ( 1857) hydrogen bonds : angle 4.70114 ( 5472) metal coordination : bond 0.00266 ( 7) metal coordination : angle 4.34749 ( 6) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7938.72 seconds wall clock time: 138 minutes 8.40 seconds (8288.40 seconds total)