Starting phenix.real_space_refine on Sun Feb 8 00:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.map" model { file = "/net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i1i_52570/02_2026/9i1i_52570.cif" } resolution = 4.5 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 6 5.49 5 Mg 1 5.21 5 S 219 5.16 5 C 23463 2.51 5 N 6336 2.21 5 O 6825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.04s 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: 36852 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 36787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4584, 36787 Classifications: {'peptide': 4584} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 189, 'TRANS': 4393} Chain breaks: 15 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: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27808 SG CYS A3962 90.005 133.248 220.932 1.00591.29 S ATOM 27972 SG CYS A3982 87.776 130.710 222.789 1.00571.51 S ATOM 27997 SG CYS A3985 91.514 131.095 223.692 1.00580.13 S ATOM 27698 SG CYS A3947 79.713 126.090 219.122 1.00419.58 S ATOM 27723 SG CYS A3950 77.383 123.154 218.005 1.00384.41 S ATOM 27851 SG CYS A3967 77.699 125.911 215.847 1.00511.47 S ATOM 27876 SG CYS A3970 76.004 126.637 219.201 1.00547.73 S Time building chain proxies: 8.12, per 1000 atoms: 0.22 Number of scatterers: 36852 At special positions: 0 Unit cell: (129.32, 153.7, 244.86, 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 219 16.00 P 6 15.00 Mg 1 11.99 O 6825 8.00 N 6336 7.00 C 23463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8764 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 20 sheets defined 60.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.726A pdb=" N LEU A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 537 removed outlier: 4.022A pdb=" N GLU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 554 through 575 removed outlier: 3.885A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 569 " --> pdb=" O HIS A 565 " (cutoff:3.500A) Proline residue: A 572 - end of helix removed outlier: 3.507A pdb=" N GLU A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 590 through 606 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.677A pdb=" N TYR A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.995A pdb=" N HIS A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 removed outlier: 3.604A 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 643 through 656 removed outlier: 3.601A pdb=" N ILE A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 removed outlier: 4.013A pdb=" N LEU A 665 " --> pdb=" O ASP A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 666 through 673 removed outlier: 4.304A pdb=" N LEU A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.673A 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: 3.912A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 4.322A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.574A pdb=" N SER A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 759 through 775 removed outlier: 4.242A 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 800 Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 810 through 827 removed outlier: 3.596A pdb=" N TYR A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 864 through 889 removed outlier: 3.511A pdb=" N PHE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 removed outlier: 3.850A pdb=" N GLU A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 4.323A pdb=" N GLN A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 4.033A 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 1009 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1033 through 1044 removed outlier: 4.065A pdb=" N ASN A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1071 Processing helix chain 'A' and resid 1079 through 1089 Processing helix chain 'A' and resid 1089 through 1102 removed outlier: 3.882A pdb=" N ARG A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1144 removed outlier: 3.801A 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 Processing helix chain 'A' and resid 1190 through 1203 removed outlier: 3.628A pdb=" N ARG A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) 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 1234 through 1241 removed outlier: 3.701A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.609A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.558A pdb=" N VAL A1266 " --> pdb=" O THR A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1298 through 1330 removed outlier: 3.705A pdb=" N ARG A1302 " --> pdb=" O TRP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1346 Processing helix chain 'A' and resid 1363 through 1369 removed outlier: 4.075A pdb=" N LEU A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1387 removed outlier: 3.793A pdb=" N LEU A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1398 removed outlier: 3.621A pdb=" N VAL A1391 " --> pdb=" O GLN A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1415 removed outlier: 4.197A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1440 removed outlier: 4.189A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (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 1487 removed outlier: 4.217A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A1487 " --> pdb=" O LYS A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1521 through 1524 Processing helix chain 'A' and resid 1544 through 1557 Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 3.692A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1658 removed outlier: 3.542A pdb=" N LEU A1634 " --> pdb=" O ASP A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1665 Processing helix chain 'A' and resid 1667 through 1678 Processing helix chain 'A' and resid 1684 through 1692 removed outlier: 3.613A pdb=" N LEU A1688 " --> pdb=" O SER A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Processing helix chain 'A' and resid 1712 through 1733 Proline residue: A1727 - end of helix removed outlier: 3.692A pdb=" N GLU A1733 " --> pdb=" O GLN A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 4.026A 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 1810 Processing helix chain 'A' and resid 1811 through 1813 No H-bonds generated for 'chain 'A' and resid 1811 through 1813' Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 3.930A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1862 Processing helix chain 'A' and resid 1863 through 1881 removed outlier: 3.525A pdb=" N ALA A1881 " --> pdb=" O LEU A1877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1905 Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1937 through 1941 removed outlier: 3.753A pdb=" N THR A1940 " --> pdb=" O SER A1937 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1937 through 1941' Processing helix chain 'A' and resid 1959 through 1974 removed outlier: 3.515A pdb=" N LYS A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1993 through 2002 removed outlier: 4.182A 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 removed outlier: 4.016A pdb=" N PHE A2031 " --> pdb=" O GLY A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2086 removed outlier: 4.020A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2099 Processing helix chain 'A' and resid 2116 through 2121 Processing helix chain 'A' and resid 2122 through 2137 Proline residue: A2128 - end of helix removed outlier: 4.282A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2167 removed outlier: 3.668A pdb=" N GLY A2167 " --> pdb=" O LEU A2163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2193 Processing helix chain 'A' and resid 2194 through 2203 Processing helix chain 'A' and resid 2207 through 2224 removed outlier: 3.649A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2255 Processing helix chain 'A' and resid 2308 through 2319 Processing helix chain 'A' and resid 2325 through 2329 removed outlier: 3.889A pdb=" N ASN A2328 " --> pdb=" O ASP A2325 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.612A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A2438 " --> pdb=" O SER A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2464 Processing helix chain 'A' and resid 2492 through 2501 Processing helix chain 'A' and resid 2509 through 2513 Processing helix chain 'A' and resid 2521 through 2525 Processing helix chain 'A' and resid 2550 through 2562 Processing helix chain 'A' and resid 2571 through 2589 removed outlier: 3.883A pdb=" N VAL A2575 " --> pdb=" O SER A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2601 through 2615 removed outlier: 4.742A pdb=" N LYS A2607 " --> pdb=" O GLU A2603 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A2608 " --> pdb=" O ARG A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2631 removed outlier: 3.584A pdb=" N LEU A2619 " --> pdb=" O HIS A2615 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A2620 " --> pdb=" O SER A2616 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A2621 " --> pdb=" O ASP A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2632 through 2636 removed outlier: 3.941A pdb=" N HIS A2635 " --> pdb=" O ASP A2632 " (cutoff:3.500A) Processing helix chain 'A' and resid 2642 through 2654 Processing helix chain 'A' and resid 2660 through 2669 Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.568A pdb=" N ASN A2677 " --> pdb=" O LYS A2674 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.806A pdb=" N ILE A2682 " --> pdb=" O SER A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2723 Processing helix chain 'A' and resid 2735 through 2747 Processing helix chain 'A' and resid 2754 through 2760 Processing helix chain 'A' and resid 2775 through 2790 removed outlier: 3.940A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2813 removed outlier: 4.140A pdb=" N ASP A2812 " --> pdb=" O LEU A2809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A2813 " --> pdb=" O ALA A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2816 through 2819 removed outlier: 3.929A pdb=" N LYS A2819 " --> pdb=" O MET A2816 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2816 through 2819' Processing helix chain 'A' and resid 2820 through 2828 removed outlier: 3.742A pdb=" N GLU A2826 " --> pdb=" O HIS A2822 " (cutoff:3.500A) Processing helix chain 'A' and resid 2853 through 2858 removed outlier: 3.754A pdb=" N ASN A2856 " --> pdb=" O ALA A2853 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A2857 " --> pdb=" O LYS A2854 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2879 removed outlier: 3.707A pdb=" N CYS A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) Processing helix chain 'A' and resid 2882 through 2890 removed outlier: 3.681A pdb=" N GLN A2886 " --> pdb=" O ASP A2882 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A2888 " --> pdb=" O LEU A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2892 through 2907 removed outlier: 3.506A pdb=" N GLN A2907 " --> pdb=" O VAL A2903 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2932 Processing helix chain 'A' and resid 2936 through 2948 removed outlier: 3.505A pdb=" N ILE A2940 " --> pdb=" O SER A2936 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2964 removed outlier: 3.652A pdb=" N SER A2963 " --> pdb=" O ILE A2959 " (cutoff:3.500A) Processing helix chain 'A' and resid 2974 through 2984 removed outlier: 3.522A pdb=" N LEU A2978 " --> pdb=" O SER A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3019 removed outlier: 3.733A 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 3113 through 3120 Processing helix chain 'A' and resid 3121 through 3127 Processing helix chain 'A' and resid 3140 through 3156 removed outlier: 3.585A pdb=" N GLU A3156 " --> pdb=" O GLN A3152 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3177 Processing helix chain 'A' and resid 3183 through 3197 removed outlier: 3.632A pdb=" N SER A3187 " --> pdb=" O ASP A3183 " (cutoff:3.500A) Processing helix chain 'A' and resid 3203 through 3219 removed outlier: 4.049A pdb=" N ARG A3207 " --> pdb=" O GLU A3203 " (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 3237 through 3248 Processing helix chain 'A' and resid 3254 through 3265 removed outlier: 3.729A pdb=" N MET A3265 " --> pdb=" O ALA A3261 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3295 removed outlier: 3.757A pdb=" N ASP A3290 " --> pdb=" O GLY A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3313 through 3327 removed outlier: 4.028A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3348 through 3365 removed outlier: 4.103A pdb=" N SER A3352 " --> pdb=" O GLN A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.941A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3422 through 3427 removed outlier: 3.785A pdb=" N LYS A3427 " --> pdb=" O GLN A3424 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3491 removed outlier: 4.988A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3513 Processing helix chain 'A' and resid 3517 through 3540 removed outlier: 3.907A 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 3593 through 3600 removed outlier: 4.248A pdb=" N LEU A3597 " --> pdb=" O GLY A3593 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A3598 " --> pdb=" O ASN A3594 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A3599 " --> pdb=" O LEU A3595 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 3.852A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3676 Processing helix chain 'A' and resid 3680 through 3692 removed outlier: 3.658A pdb=" N THR A3692 " --> pdb=" O ILE A3688 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3700 removed outlier: 3.877A pdb=" N GLN A3700 " --> pdb=" O VAL A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3702 through 3722 Processing helix chain 'A' and resid 3727 through 3745 Processing helix chain 'A' and resid 3761 through 3785 removed outlier: 4.110A pdb=" N HIS A3765 " --> pdb=" O LEU A3761 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS A3785 " --> pdb=" O ILE A3781 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 4.227A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A3794 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A3796 " --> pdb=" O LEU A3792 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3823 removed outlier: 4.122A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3839 Processing helix chain 'A' and resid 3839 through 3847 Processing helix chain 'A' and resid 3856 through 3890 removed outlier: 4.485A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3894 through 3908 Processing helix chain 'A' and resid 3917 through 3940 removed outlier: 3.943A 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 4026 Processing helix chain 'A' and resid 4027 through 4029 No H-bonds generated for 'chain 'A' and resid 4027 through 4029' Processing helix chain 'A' and resid 4035 through 4045 removed outlier: 3.529A pdb=" N ILE A4039 " --> pdb=" O GLU A4035 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4090 Processing helix chain 'A' and resid 4092 through 4095 Processing helix chain 'A' and resid 4096 through 4111 Processing helix chain 'A' and resid 4116 through 4139 removed outlier: 4.214A pdb=" N LEU A4120 " --> pdb=" O ASP A4116 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4156 removed outlier: 4.226A pdb=" N VAL A4146 " --> pdb=" O ASN A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4171 through 4198 Processing helix chain 'A' and resid 4204 through 4219 Processing helix chain 'A' and resid 4221 through 4236 removed outlier: 4.223A pdb=" N ARG A4225 " --> pdb=" O ASN A4221 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4245 removed outlier: 3.923A pdb=" N VAL A4241 " --> pdb=" O GLY A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4255 Processing helix chain 'A' and resid 4257 through 4262 removed outlier: 3.577A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A4262 " --> pdb=" O LYS A4258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4257 through 4262' Processing helix chain 'A' and resid 4279 through 4293 Processing helix chain 'A' and resid 4296 through 4305 removed outlier: 4.324A 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 4342 through 4353 Processing helix chain 'A' and resid 4358 through 4370 removed outlier: 3.801A 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 4407 through 4417 removed outlier: 4.324A pdb=" N LEU A4411 " --> pdb=" O ILE A4407 " (cutoff:3.500A) Processing helix chain 'A' and resid 4522 through 4542 Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 3.703A pdb=" N LEU A4548 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4576 removed outlier: 3.795A pdb=" N PHE A4562 " --> pdb=" O ASP A4558 " (cutoff:3.500A) Processing helix chain 'A' and resid 4581 through 4596 removed outlier: 3.519A pdb=" N LEU A4596 " --> pdb=" O ILE A4592 " (cutoff:3.500A) Processing helix chain 'A' and resid 4597 through 4599 No H-bonds generated for 'chain 'A' and resid 4597 through 4599' Processing helix chain 'A' and resid 4613 through 4633 Processing helix chain 'A' and resid 4638 through 4648 Processing helix chain 'A' and resid 4665 through 4669 removed outlier: 4.246A pdb=" N PHE A4668 " --> pdb=" O PRO A4665 " (cutoff:3.500A) Processing helix chain 'A' and resid 4691 through 4702 Processing helix chain 'A' and resid 4708 through 4717 removed outlier: 3.633A pdb=" N TRP A4712 " --> pdb=" O VAL A4708 " (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 4809 through 4813 Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 4.211A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4871 through 4878 removed outlier: 3.852A pdb=" N LEU A4875 " --> pdb=" O ASP A4871 " (cutoff:3.500A) Processing helix chain 'A' and resid 4895 through 4905 removed outlier: 3.732A pdb=" N ILE A4899 " --> pdb=" O ASP A4895 " (cutoff:3.500A) Processing helix chain 'A' and resid 4930 through 4941 Processing helix chain 'A' and resid 4947 through 4958 Processing helix chain 'A' and resid 4961 through 4980 removed outlier: 3.778A 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: 3.688A 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 removed outlier: 3.537A pdb=" N TYR A5048 " --> pdb=" O ASP A5045 " (cutoff:3.500A) Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.123A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 3.604A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5099 through 5108 Processing helix chain 'A' and resid 5116 through 5121 Processing helix chain 'A' and resid 5131 through 5149 removed outlier: 3.946A pdb=" N TRP A5135 " --> pdb=" O CYS A5131 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A5149 " --> pdb=" O ARG A5145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 434 removed outlier: 4.164A pdb=" N VAL A 369 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 386 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY A 373 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 384 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N ALA A 385 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP A 406 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU A 387 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS A 404 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 400 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 393 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 398 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N THR A 347 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 12.091A pdb=" N HIS A 465 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N THR A 349 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N TYR A 467 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N TYR A 351 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N ASP A 469 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N HIS A 353 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE A 471 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 355 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 434 removed outlier: 4.014A pdb=" N CYS A 451 " --> pdb=" O MET A 539 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET A 539 " --> pdb=" O CYS A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1148 through 1151 removed outlier: 5.979A pdb=" N GLN A1149 " --> pdb=" O VAL A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1541 through 1543 removed outlier: 3.656A pdb=" N LEU A1625 " --> pdb=" O MET A1615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1793 through 1796 removed outlier: 6.123A pdb=" N ASN A1793 " --> pdb=" O ILE A1890 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS A1892 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A1795 " --> pdb=" O CYS A1892 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2057 through 2062 removed outlier: 6.922A pdb=" N GLY A1949 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A2061 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A1951 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1984 through 1987 removed outlier: 5.512A pdb=" N ILE A1985 " --> pdb=" O ASP A2019 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2040 through 2041 Processing sheet with id=AA9, first strand: chain 'A' and resid 2266 through 2269 removed outlier: 3.605A pdb=" N THR A2277 " --> pdb=" O PHE A2268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id=AB2, first strand: chain 'A' and resid 2377 through 2380 removed outlier: 4.414A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A2408 " --> pdb=" O PHE A2446 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP A2448 " --> pdb=" O LYS A2408 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A2410 " --> pdb=" O ASP A2448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB4, first strand: chain 'A' and resid 2762 through 2763 removed outlier: 6.187A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 2766 through 2767 removed outlier: 3.672A pdb=" N VAL A2803 " --> pdb=" O VAL A2766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3026 through 3027 removed outlier: 6.415A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A3002 " --> pdb=" O VAL A3109 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU A3111 " --> pdb=" O LEU A3002 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A3004 " --> pdb=" O GLU A3111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3086 through 3091 removed outlier: 4.375A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 5.696A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ARG A3397 " --> pdb=" O ALA A3272 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A3274 " --> pdb=" O ARG A3397 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A3401 " --> pdb=" O GLU A3276 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR A3278 " --> pdb=" O ILE A3401 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3958 through 3959 removed outlier: 3.841A pdb=" N VAL A3958 " --> pdb=" O TYR A3966 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A3966 " --> pdb=" O VAL A3958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 4852 through 4853 removed outlier: 3.711A pdb=" N VAL A4853 " --> pdb=" O ARG A4913 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 4881 through 4883 1862 hydrogen bonds defined for protein. 5430 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: 12.91 Time building geometry restraints manager: 4.69 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: 12050 1.34 - 1.46: 7492 1.46 - 1.58: 17754 1.58 - 1.70: 5 1.70 - 1.82: 322 Bond restraints: 37623 Sorted by residual: bond pdb=" CA GLY A3394 " pdb=" C GLY A3394 " ideal model delta sigma weight residual 1.530 1.503 0.027 1.04e-02 9.25e+03 6.84e+00 bond pdb=" C LEU A2599 " pdb=" N ARG A2600 " ideal model delta sigma weight residual 1.332 1.313 0.020 1.40e-02 5.10e+03 2.02e+00 bond pdb=" CG GLN A3955 " pdb=" CD GLN A3955 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" N GLY A3394 " pdb=" CA GLY A3394 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.86e+00 bond pdb=" CB ASN A1014 " pdb=" CG ASN A1014 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.71e+00 ... (remaining 37618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 50544 3.31 - 6.63: 318 6.63 - 9.94: 37 9.94 - 13.25: 6 13.25 - 16.56: 3 Bond angle restraints: 50908 Sorted by residual: angle pdb=" C ARG A2051 " pdb=" N SER A2052 " pdb=" CA SER A2052 " ideal model delta sigma weight residual 122.38 105.82 16.56 2.90e+00 1.19e-01 3.26e+01 angle pdb=" CA ARG A1377 " pdb=" CB ARG A1377 " pdb=" CG ARG A1377 " ideal model delta sigma weight residual 114.10 123.96 -9.86 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CA LEU A3714 " pdb=" CB LEU A3714 " pdb=" CG LEU A3714 " ideal model delta sigma weight residual 116.30 132.64 -16.34 3.50e+00 8.16e-02 2.18e+01 angle pdb=" N GLY A1071 " pdb=" CA GLY A1071 " pdb=" C GLY A1071 " ideal model delta sigma weight residual 115.32 109.27 6.05 1.31e+00 5.83e-01 2.13e+01 angle pdb=" CA LEU A1256 " pdb=" CB LEU A1256 " pdb=" CG LEU A1256 " ideal model delta sigma weight residual 116.30 131.39 -15.09 3.50e+00 8.16e-02 1.86e+01 ... (remaining 50903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19957 17.91 - 35.83: 2281 35.83 - 53.74: 550 53.74 - 71.66: 84 71.66 - 89.57: 50 Dihedral angle restraints: 22922 sinusoidal: 9452 harmonic: 13470 Sorted by residual: dihedral pdb=" CB CYS A 951 " pdb=" SG CYS A 951 " pdb=" SG CYS A 992 " pdb=" CB CYS A 992 " ideal model delta sinusoidal sigma weight residual -86.00 -143.57 57.57 1 1.00e+01 1.00e-02 4.45e+01 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 -147.42 -32.58 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA VAL A2024 " pdb=" C VAL A2024 " pdb=" N GLN A2025 " pdb=" CA GLN A2025 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 22919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4951 0.063 - 0.127: 734 0.127 - 0.190: 36 0.190 - 0.253: 1 0.253 - 0.316: 4 Chirality restraints: 5726 Sorted by residual: chirality pdb=" CG LEU A3714 " pdb=" CB LEU A3714 " pdb=" CD1 LEU A3714 " pdb=" CD2 LEU A3714 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CG LEU A1803 " pdb=" CB LEU A1803 " pdb=" CD1 LEU A1803 " pdb=" CD2 LEU A1803 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A1256 " pdb=" CB LEU A1256 " pdb=" CD1 LEU A1256 " pdb=" CD2 LEU A1256 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 5723 not shown) Planarity restraints: 6505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A3832 " -0.024 2.00e-02 2.50e+03 1.83e-02 8.34e+00 pdb=" CG TRP A3832 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A3832 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A3832 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A3832 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A3832 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A3832 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3832 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3832 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A3832 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A3955 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" CD GLN A3955 " -0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A3955 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN A3955 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1377 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ARG A1377 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG A1377 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A1378 " 0.015 2.00e-02 2.50e+03 ... (remaining 6502 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 636 2.64 - 3.21: 36393 3.21 - 3.77: 60728 3.77 - 4.34: 78692 4.34 - 4.90: 126145 Nonbonded interactions: 302594 Sorted by model distance: nonbonded pdb=" O HIS A1564 " pdb=" OG1 THR A1568 " model vdw 2.079 3.040 nonbonded pdb=" OD1 ASP A3413 " pdb=" OG1 THR A3415 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR A2357 " pdb=" OD1 ASP A2359 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A2583 " pdb=" OH TYR A2664 " model vdw 2.147 3.040 nonbonded pdb=" O LEU A4089 " pdb=" OG SER A4131 " model vdw 2.172 3.040 ... (remaining 302589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.840 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 44.700 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.901 37635 Z= 0.645 Angle : 0.737 16.565 50921 Z= 0.380 Chirality : 0.043 0.316 5726 Planarity : 0.004 0.075 6505 Dihedral : 16.319 89.572 14152 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.75 % Favored : 92.22 % Rotamer: Outliers : 1.63 % Allowed : 18.00 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4552 helix: 0.40 (0.11), residues: 2462 sheet: -1.28 (0.29), residues: 293 loop : -2.08 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1377 TYR 0.019 0.002 TYR A2654 PHE 0.029 0.002 PHE A2433 TRP 0.049 0.002 TRP A3832 HIS 0.013 0.001 HIS A3268 Details of bonding type rmsd covalent geometry : bond 0.00351 (37623) covalent geometry : angle 0.73147 (50908) SS BOND : bond 0.00264 ( 2) SS BOND : angle 1.39963 ( 4) hydrogen bonds : bond 0.13072 ( 1860) hydrogen bonds : angle 6.00025 ( 5430) metal coordination : bond 0.17149 ( 8) metal coordination : angle 7.06720 ( 9) Misc. bond : bond 0.84773 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 419 time to evaluate : 1.539 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 405 MET cc_start: 0.4928 (tmm) cc_final: 0.4355 (ptt) REVERT: A 664 TRP cc_start: 0.8513 (p-90) cc_final: 0.7508 (p-90) REVERT: A 772 LEU cc_start: 0.8981 (tt) cc_final: 0.8774 (tt) REVERT: A 868 ASP cc_start: 0.8793 (m-30) cc_final: 0.8586 (m-30) REVERT: A 922 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8446 (mm-30) REVERT: A 1087 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8855 (pp) REVERT: A 1233 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 1442 MET cc_start: 0.6882 (tpt) cc_final: 0.6348 (tpt) REVERT: A 1547 GLU cc_start: 0.8737 (tt0) cc_final: 0.8208 (mt-10) REVERT: A 1552 LEU cc_start: 0.9750 (tt) cc_final: 0.9548 (tp) REVERT: A 1615 MET cc_start: 0.9095 (mmm) cc_final: 0.8594 (mmm) REVERT: A 1620 GLU cc_start: 0.6929 (pm20) cc_final: 0.6274 (pm20) REVERT: A 1751 MET cc_start: 0.7491 (tpp) cc_final: 0.7064 (tmm) REVERT: A 1764 LEU cc_start: 0.9154 (mt) cc_final: 0.8562 (mt) REVERT: A 2012 MET cc_start: 0.8677 (tpt) cc_final: 0.8422 (ppp) REVERT: A 2102 MET cc_start: -0.1206 (ppp) cc_final: -0.1877 (pmm) REVERT: A 2135 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 2216 MET cc_start: 0.9082 (mmt) cc_final: 0.8466 (tpp) REVERT: A 2276 MET cc_start: 0.3054 (mmp) cc_final: 0.2059 (mmp) REVERT: A 2307 MET cc_start: 0.4075 (OUTLIER) cc_final: 0.3533 (ppp) REVERT: A 2747 MET cc_start: 0.9448 (ttm) cc_final: 0.9116 (ttp) REVERT: A 2816 MET cc_start: 0.8765 (mmp) cc_final: 0.8494 (ppp) REVERT: A 3111 GLU cc_start: 0.8512 (tp30) cc_final: 0.7945 (mm-30) REVERT: A 3114 ASP cc_start: 0.8976 (p0) cc_final: 0.8771 (t0) REVERT: A 3216 ILE cc_start: 0.9025 (mt) cc_final: 0.8770 (mm) REVERT: A 3560 LEU cc_start: 0.8704 (mt) cc_final: 0.8366 (mt) REVERT: A 4001 HIS cc_start: 0.7887 (m90) cc_final: 0.7470 (m170) REVERT: A 4113 LEU cc_start: 0.7413 (mp) cc_final: 0.7081 (pt) REVERT: A 4304 MET cc_start: 0.8785 (mmm) cc_final: 0.8494 (mmm) REVERT: A 4429 MET cc_start: 0.2726 (mmt) cc_final: 0.1865 (mmt) REVERT: A 4694 TYR cc_start: 0.9287 (t80) cc_final: 0.8898 (t80) REVERT: A 4695 LEU cc_start: 0.9411 (mm) cc_final: 0.9201 (mm) REVERT: A 5007 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8231 (pp) REVERT: A 5037 ASN cc_start: 0.8839 (m-40) cc_final: 0.8547 (p0) REVERT: A 5082 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8900 (mm) outliers start: 67 outliers final: 12 residues processed: 469 average time/residue: 0.2535 time to fit residues: 192.3551 Evaluate side-chains 275 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.0020 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 overall best weight: 4.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN A1295 GLN A1849 GLN A1926 GLN ** A1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1995 ASN ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2785 GLN ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4608 ASN ** A4757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4759 HIS ** A4883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 GLN ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.047830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.035903 restraints weight = 411236.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.036800 restraints weight = 294826.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.037493 restraints weight = 231634.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.038016 restraints weight = 191373.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.038337 restraints weight = 164587.778| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37635 Z= 0.216 Angle : 0.742 11.520 50921 Z= 0.380 Chirality : 0.045 0.200 5726 Planarity : 0.005 0.080 6505 Dihedral : 6.042 83.485 5022 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.71 % Favored : 92.27 % Rotamer: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.95 (0.12), residues: 4552 helix: 0.37 (0.10), residues: 2510 sheet: -1.46 (0.27), residues: 317 loop : -1.93 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A4530 TYR 0.037 0.002 TYR A 553 PHE 0.044 0.003 PHE A3939 TRP 0.038 0.002 TRP A1031 HIS 0.012 0.002 HIS A1207 Details of bonding type rmsd covalent geometry : bond 0.00455 (37623) covalent geometry : angle 0.73952 (50908) SS BOND : bond 0.00424 ( 2) SS BOND : angle 1.33195 ( 4) hydrogen bonds : bond 0.04048 ( 1860) hydrogen bonds : angle 4.89731 ( 5430) metal coordination : bond 0.00519 ( 8) metal coordination : angle 4.88670 ( 9) Misc. bond : bond 0.00407 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 312 time to evaluate : 1.513 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 508 ARG cc_start: 0.8524 (tmm160) cc_final: 0.8202 (tmt170) REVERT: A 675 MET cc_start: 0.7515 (mpp) cc_final: 0.7218 (mpp) REVERT: A 703 PHE cc_start: 0.8247 (m-10) cc_final: 0.7987 (m-80) REVERT: A 973 ILE cc_start: 0.8306 (pt) cc_final: 0.8088 (mt) REVERT: A 978 SER cc_start: 0.9057 (t) cc_final: 0.8774 (p) REVERT: A 1082 GLN cc_start: 0.8617 (mp10) cc_final: 0.8378 (pm20) REVERT: A 1398 LEU cc_start: 0.8920 (tp) cc_final: 0.8655 (tp) REVERT: A 1442 MET cc_start: 0.6834 (tpt) cc_final: 0.6551 (tpt) REVERT: A 1550 GLU cc_start: 0.9321 (pt0) cc_final: 0.9086 (pp20) REVERT: A 1551 LEU cc_start: 0.9804 (tt) cc_final: 0.9515 (tt) REVERT: A 1615 MET cc_start: 0.9179 (mmm) cc_final: 0.8733 (mpp) REVERT: A 1620 GLU cc_start: 0.7602 (pm20) cc_final: 0.7203 (pm20) REVERT: A 1751 MET cc_start: 0.8462 (tpp) cc_final: 0.7948 (tmm) REVERT: A 1811 MET cc_start: 0.8013 (mtp) cc_final: 0.7752 (mtp) REVERT: A 2012 MET cc_start: 0.9050 (tpt) cc_final: 0.8529 (ppp) REVERT: A 2102 MET cc_start: -0.1206 (ppp) cc_final: -0.1898 (pmm) REVERT: A 2216 MET cc_start: 0.9632 (mmt) cc_final: 0.9264 (tpt) REVERT: A 2274 MET cc_start: 0.7016 (tpt) cc_final: 0.6749 (tpt) REVERT: A 2276 MET cc_start: 0.5137 (mmp) cc_final: 0.4518 (mmp) REVERT: A 2307 MET cc_start: 0.5132 (ppp) cc_final: 0.3251 (ppp) REVERT: A 2361 MET cc_start: 0.9492 (mtm) cc_final: 0.9069 (mtt) REVERT: A 2715 MET cc_start: 0.9375 (mmp) cc_final: 0.9147 (mmm) REVERT: A 2716 MET cc_start: 0.9471 (mtt) cc_final: 0.9161 (ttm) REVERT: A 2747 MET cc_start: 0.9448 (ttm) cc_final: 0.9056 (ttm) REVERT: A 2923 MET cc_start: 0.9272 (ptp) cc_final: 0.9040 (ptt) REVERT: A 3073 ASP cc_start: 0.9475 (m-30) cc_final: 0.9269 (m-30) REVERT: A 3111 GLU cc_start: 0.9242 (tp30) cc_final: 0.8783 (mm-30) REVERT: A 3382 MET cc_start: 0.7191 (mmp) cc_final: 0.6683 (mmm) REVERT: A 3479 ARG cc_start: 0.9397 (tpp-160) cc_final: 0.9147 (mmm160) REVERT: A 3612 MET cc_start: 0.9092 (mmp) cc_final: 0.8741 (mtt) REVERT: A 3613 PHE cc_start: 0.8659 (t80) cc_final: 0.8442 (t80) REVERT: A 3731 MET cc_start: 0.9181 (mmp) cc_final: 0.8940 (tmm) REVERT: A 3735 MET cc_start: 0.9181 (ptt) cc_final: 0.8966 (ptt) REVERT: A 3925 MET cc_start: 0.9259 (mtt) cc_final: 0.8824 (tpp) REVERT: A 3981 MET cc_start: 0.6475 (ppp) cc_final: 0.6007 (ppp) REVERT: A 4238 MET cc_start: 0.8266 (pmm) cc_final: 0.7668 (pmm) REVERT: A 4341 LYS cc_start: 0.9198 (mppt) cc_final: 0.8775 (tptp) REVERT: A 4429 MET cc_start: 0.2666 (mmt) cc_final: 0.2031 (mmt) REVERT: A 4694 TYR cc_start: 0.9493 (t80) cc_final: 0.9017 (t80) REVERT: A 4695 LEU cc_start: 0.9450 (mm) cc_final: 0.9213 (mm) outliers start: 4 outliers final: 0 residues processed: 315 average time/residue: 0.2273 time to fit residues: 118.3022 Evaluate side-chains 232 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 391 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 456 optimal weight: 2.9990 chunk 396 optimal weight: 10.0000 chunk 431 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 289 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 514 GLN A1146 HIS A1295 GLN ** A1433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3077 GLN ** A3095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3671 GLN A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4010 GLN A4145 GLN ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.046699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.034774 restraints weight = 416643.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.035715 restraints weight = 294362.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.036448 restraints weight = 228815.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.036893 restraints weight = 188999.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.037276 restraints weight = 164089.235| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 37635 Z= 0.180 Angle : 0.666 11.232 50921 Z= 0.340 Chirality : 0.043 0.295 5726 Planarity : 0.004 0.063 6505 Dihedral : 5.817 73.043 5022 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.69 % Favored : 92.29 % Rotamer: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.78 (0.12), residues: 4552 helix: 0.50 (0.10), residues: 2521 sheet: -1.18 (0.28), residues: 299 loop : -1.90 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2968 TYR 0.022 0.002 TYR A3652 PHE 0.025 0.002 PHE A3939 TRP 0.026 0.002 TRP A1031 HIS 0.010 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00383 (37623) covalent geometry : angle 0.66392 (50908) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.30310 ( 4) hydrogen bonds : bond 0.03743 ( 1860) hydrogen bonds : angle 4.70472 ( 5430) metal coordination : bond 0.00594 ( 8) metal coordination : angle 4.02333 ( 9) Misc. bond : bond 0.00320 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.102 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: A 675 MET cc_start: 0.7485 (mpp) cc_final: 0.7093 (mpp) REVERT: A 903 LEU cc_start: 0.7354 (mt) cc_final: 0.6916 (tp) REVERT: A 973 ILE cc_start: 0.8340 (pt) cc_final: 0.8109 (mt) REVERT: A 1398 LEU cc_start: 0.8864 (tp) cc_final: 0.8591 (tp) REVERT: A 1442 MET cc_start: 0.7171 (tpt) cc_final: 0.6882 (tpt) REVERT: A 1546 GLU cc_start: 0.9184 (pm20) cc_final: 0.8859 (pm20) REVERT: A 1548 LEU cc_start: 0.9438 (mt) cc_final: 0.9219 (mt) REVERT: A 1550 GLU cc_start: 0.9312 (pt0) cc_final: 0.9057 (pp20) REVERT: A 1551 LEU cc_start: 0.9816 (tt) cc_final: 0.9570 (tp) REVERT: A 1620 GLU cc_start: 0.7544 (pm20) cc_final: 0.7215 (pm20) REVERT: A 1737 MET cc_start: 0.9262 (mpp) cc_final: 0.9004 (mpp) REVERT: A 1811 MET cc_start: 0.7841 (mtp) cc_final: 0.7556 (mtp) REVERT: A 2012 MET cc_start: 0.9063 (tpt) cc_final: 0.8571 (ppp) REVERT: A 2042 MET cc_start: 0.7858 (tmm) cc_final: 0.7636 (tmm) REVERT: A 2102 MET cc_start: -0.1513 (ppp) cc_final: -0.2257 (pmm) REVERT: A 2219 MET cc_start: 0.8398 (ptp) cc_final: 0.7784 (mtm) REVERT: A 2274 MET cc_start: 0.7076 (tpt) cc_final: 0.6636 (tpt) REVERT: A 2276 MET cc_start: 0.5426 (mmp) cc_final: 0.4588 (mmp) REVERT: A 2307 MET cc_start: 0.5153 (ppp) cc_final: 0.3279 (ppp) REVERT: A 2361 MET cc_start: 0.9480 (mtm) cc_final: 0.9006 (mtt) REVERT: A 2648 MET cc_start: 0.5263 (mmp) cc_final: 0.5055 (mmt) REVERT: A 2715 MET cc_start: 0.9162 (mmp) cc_final: 0.8916 (mmm) REVERT: A 2716 MET cc_start: 0.9546 (mtt) cc_final: 0.9331 (mtp) REVERT: A 2747 MET cc_start: 0.9613 (ttm) cc_final: 0.9119 (ttm) REVERT: A 3382 MET cc_start: 0.7465 (mmp) cc_final: 0.6671 (mmm) REVERT: A 3479 ARG cc_start: 0.9324 (tpp-160) cc_final: 0.9084 (mmm160) REVERT: A 3529 MET cc_start: 0.8981 (mpp) cc_final: 0.8574 (mpp) REVERT: A 3612 MET cc_start: 0.9025 (mmp) cc_final: 0.8552 (mtt) REVERT: A 3613 PHE cc_start: 0.8560 (t80) cc_final: 0.8262 (t80) REVERT: A 3735 MET cc_start: 0.9074 (ptt) cc_final: 0.8847 (ptt) REVERT: A 3819 MET cc_start: 0.9322 (ptp) cc_final: 0.8913 (ptp) REVERT: A 4238 MET cc_start: 0.8236 (pmm) cc_final: 0.7644 (pmm) REVERT: A 4304 MET cc_start: 0.8889 (mmp) cc_final: 0.8658 (mmp) REVERT: A 4341 LYS cc_start: 0.9252 (mppt) cc_final: 0.8878 (tptp) REVERT: A 4392 MET cc_start: 0.9214 (mmm) cc_final: 0.8759 (mmm) REVERT: A 4429 MET cc_start: 0.2421 (mmt) cc_final: 0.1685 (mmt) REVERT: A 4694 TYR cc_start: 0.9442 (t80) cc_final: 0.8928 (t80) REVERT: A 4695 LEU cc_start: 0.9451 (mm) cc_final: 0.9201 (mm) REVERT: A 5079 MET cc_start: 0.7237 (tpp) cc_final: 0.7008 (tpp) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.2208 time to fit residues: 108.0711 Evaluate side-chains 218 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 409 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 424 optimal weight: 0.3980 chunk 330 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 249 optimal weight: 0.1980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 643 GLN A1295 GLN A1433 GLN A1581 GLN ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2413 HIS A2439 HIS A2530 HIS ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2748 GLN ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3700 GLN A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4500 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 GLN A4862 HIS ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.035089 restraints weight = 410271.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.035956 restraints weight = 290802.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.036606 restraints weight = 226877.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.037153 restraints weight = 186609.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.037454 restraints weight = 160860.000| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37635 Z= 0.142 Angle : 0.639 12.245 50921 Z= 0.322 Chirality : 0.042 0.255 5726 Planarity : 0.004 0.057 6505 Dihedral : 5.776 86.751 5022 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.62 % Favored : 92.36 % Rotamer: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: 4552 helix: 0.59 (0.10), residues: 2527 sheet: -1.20 (0.28), residues: 309 loop : -1.88 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3505 TYR 0.019 0.001 TYR A1854 PHE 0.029 0.002 PHE A3120 TRP 0.017 0.001 TRP A1031 HIS 0.008 0.001 HIS A4503 Details of bonding type rmsd covalent geometry : bond 0.00306 (37623) covalent geometry : angle 0.63742 (50908) SS BOND : bond 0.01566 ( 2) SS BOND : angle 2.18468 ( 4) hydrogen bonds : bond 0.03446 ( 1860) hydrogen bonds : angle 4.56182 ( 5430) metal coordination : bond 0.00398 ( 8) metal coordination : angle 3.47376 ( 9) Misc. bond : bond 0.00409 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.568 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: A 500 GLN cc_start: 0.7693 (mm110) cc_final: 0.7316 (pt0) REVERT: A 664 TRP cc_start: 0.8862 (p-90) cc_final: 0.7837 (p-90) REVERT: A 675 MET cc_start: 0.7398 (mpp) cc_final: 0.6967 (mpp) REVERT: A 868 ASP cc_start: 0.8679 (m-30) cc_final: 0.8463 (m-30) REVERT: A 903 LEU cc_start: 0.7248 (mt) cc_final: 0.6866 (tp) REVERT: A 973 ILE cc_start: 0.8402 (pt) cc_final: 0.8183 (mt) REVERT: A 1025 PHE cc_start: 0.9650 (t80) cc_final: 0.9440 (t80) REVERT: A 1375 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8833 (mp0) REVERT: A 1442 MET cc_start: 0.7335 (tpt) cc_final: 0.5705 (mmm) REVERT: A 1548 LEU cc_start: 0.9394 (mt) cc_final: 0.9192 (mt) REVERT: A 1550 GLU cc_start: 0.9258 (pt0) cc_final: 0.9005 (pp20) REVERT: A 1551 LEU cc_start: 0.9810 (tt) cc_final: 0.9553 (tp) REVERT: A 1596 MET cc_start: 0.9206 (mmp) cc_final: 0.8518 (mpp) REVERT: A 1615 MET cc_start: 0.8771 (mpp) cc_final: 0.8018 (mpp) REVERT: A 1620 GLU cc_start: 0.7507 (pm20) cc_final: 0.7209 (pm20) REVERT: A 1811 MET cc_start: 0.8003 (mtp) cc_final: 0.7721 (mtp) REVERT: A 2012 MET cc_start: 0.8999 (tpt) cc_final: 0.8512 (ppp) REVERT: A 2042 MET cc_start: 0.7856 (tmm) cc_final: 0.7603 (tmm) REVERT: A 2102 MET cc_start: -0.1570 (ppp) cc_final: -0.2736 (ptp) REVERT: A 2219 MET cc_start: 0.8235 (ptp) cc_final: 0.7723 (mtm) REVERT: A 2274 MET cc_start: 0.6889 (tpt) cc_final: 0.6493 (tpt) REVERT: A 2276 MET cc_start: 0.4980 (mmp) cc_final: 0.4402 (mmp) REVERT: A 2307 MET cc_start: 0.5274 (ppp) cc_final: 0.3490 (ppp) REVERT: A 2361 MET cc_start: 0.9512 (mtm) cc_final: 0.9065 (mtt) REVERT: A 2648 MET cc_start: 0.5375 (mmp) cc_final: 0.5142 (mmt) REVERT: A 2715 MET cc_start: 0.9148 (mmp) cc_final: 0.8912 (mmm) REVERT: A 2716 MET cc_start: 0.9531 (mtt) cc_final: 0.9319 (mtp) REVERT: A 2747 MET cc_start: 0.9556 (ttm) cc_final: 0.9059 (ttm) REVERT: A 2917 TYR cc_start: 0.8543 (t80) cc_final: 0.8334 (t80) REVERT: A 3049 VAL cc_start: 0.9815 (t) cc_final: 0.9542 (t) REVERT: A 3382 MET cc_start: 0.7273 (mmp) cc_final: 0.6553 (mmm) REVERT: A 3479 ARG cc_start: 0.9283 (tpp-160) cc_final: 0.9021 (mmm160) REVERT: A 3612 MET cc_start: 0.9030 (mmp) cc_final: 0.8622 (mtt) REVERT: A 3731 MET cc_start: 0.8808 (tmm) cc_final: 0.8195 (tmm) REVERT: A 3819 MET cc_start: 0.9200 (ptp) cc_final: 0.8861 (ptp) REVERT: A 4238 MET cc_start: 0.8225 (pmm) cc_final: 0.7637 (pmm) REVERT: A 4304 MET cc_start: 0.8872 (mmp) cc_final: 0.8625 (mmp) REVERT: A 4341 LYS cc_start: 0.9206 (mppt) cc_final: 0.8836 (tptp) REVERT: A 4429 MET cc_start: 0.2078 (mmt) cc_final: 0.1516 (mmt) REVERT: A 4694 TYR cc_start: 0.9423 (t80) cc_final: 0.8880 (t80) REVERT: A 4695 LEU cc_start: 0.9423 (mm) cc_final: 0.9140 (mm) REVERT: A 5079 MET cc_start: 0.7452 (tpp) cc_final: 0.7130 (tpp) outliers start: 2 outliers final: 2 residues processed: 283 average time/residue: 0.2296 time to fit residues: 109.8180 Evaluate side-chains 225 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 405 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 397 optimal weight: 5.9990 chunk 224 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 428 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 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 392 GLN A 541 HIS ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN A1295 GLN A1310 HIS ** A1968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2160 GLN ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2748 GLN A2947 ASN ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3095 HIS A3337 GLN ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3600 GLN ** A3705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4817 GLN ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.044937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.033491 restraints weight = 420573.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.034342 restraints weight = 306350.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.034947 restraints weight = 241070.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.035419 restraints weight = 202413.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.035769 restraints weight = 175084.361| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37635 Z= 0.208 Angle : 0.706 13.216 50921 Z= 0.360 Chirality : 0.044 0.277 5726 Planarity : 0.005 0.057 6505 Dihedral : 5.930 80.934 5022 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.87 (0.12), residues: 4552 helix: 0.41 (0.10), residues: 2525 sheet: -1.15 (0.28), residues: 289 loop : -1.93 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 725 TYR 0.018 0.002 TYR A3652 PHE 0.053 0.002 PHE A4018 TRP 0.025 0.002 TRP A 884 HIS 0.014 0.002 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00436 (37623) covalent geometry : angle 0.70475 (50908) SS BOND : bond 0.02138 ( 2) SS BOND : angle 2.16028 ( 4) hydrogen bonds : bond 0.03812 ( 1860) hydrogen bonds : angle 4.76290 ( 5430) metal coordination : bond 0.00511 ( 8) metal coordination : angle 3.41050 ( 9) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.535 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: A 721 MET cc_start: 0.8753 (mmp) cc_final: 0.8499 (mmm) REVERT: A 867 GLU cc_start: 0.9504 (mp0) cc_final: 0.9280 (mp0) REVERT: A 868 ASP cc_start: 0.8678 (m-30) cc_final: 0.8459 (m-30) REVERT: A 903 LEU cc_start: 0.7638 (mt) cc_final: 0.7179 (tp) REVERT: A 973 ILE cc_start: 0.8490 (pt) cc_final: 0.8271 (mt) REVERT: A 1442 MET cc_start: 0.7506 (tpt) cc_final: 0.5951 (mmm) REVERT: A 1547 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 1615 MET cc_start: 0.8909 (mpp) cc_final: 0.8132 (mpp) REVERT: A 1620 GLU cc_start: 0.7309 (pm20) cc_final: 0.7078 (pm20) REVERT: A 1737 MET cc_start: 0.9571 (mpp) cc_final: 0.9245 (mpp) REVERT: A 1751 MET cc_start: 0.8452 (tpp) cc_final: 0.7905 (tmm) REVERT: A 1811 MET cc_start: 0.8043 (mtp) cc_final: 0.7724 (mtp) REVERT: A 2012 MET cc_start: 0.9054 (tpt) cc_final: 0.8549 (ppp) REVERT: A 2042 MET cc_start: 0.8194 (tmm) cc_final: 0.7854 (tmm) REVERT: A 2102 MET cc_start: -0.1922 (ppp) cc_final: -0.2312 (ptp) REVERT: A 2216 MET cc_start: 0.9445 (mmp) cc_final: 0.9083 (tpt) REVERT: A 2274 MET cc_start: 0.7449 (tpt) cc_final: 0.7076 (tpt) REVERT: A 2276 MET cc_start: 0.5697 (mmp) cc_final: 0.5099 (mmp) REVERT: A 2307 MET cc_start: 0.5862 (ppp) cc_final: 0.4337 (ppp) REVERT: A 2361 MET cc_start: 0.9576 (mtm) cc_final: 0.9123 (mtt) REVERT: A 2648 MET cc_start: 0.5717 (mmp) cc_final: 0.5229 (mmt) REVERT: A 2715 MET cc_start: 0.9212 (mmp) cc_final: 0.8962 (mmm) REVERT: A 2716 MET cc_start: 0.9555 (mtt) cc_final: 0.9337 (mtp) REVERT: A 2747 MET cc_start: 0.9662 (ttm) cc_final: 0.9243 (ttm) REVERT: A 2805 ASP cc_start: 0.8201 (t0) cc_final: 0.7562 (t0) REVERT: A 2917 TYR cc_start: 0.8698 (t80) cc_final: 0.8450 (t80) REVERT: A 2923 MET cc_start: 0.9070 (ptm) cc_final: 0.8846 (ptm) REVERT: A 3049 VAL cc_start: 0.9848 (t) cc_final: 0.9559 (t) REVERT: A 3073 ASP cc_start: 0.9412 (m-30) cc_final: 0.9170 (m-30) REVERT: A 3382 MET cc_start: 0.7342 (mmp) cc_final: 0.6588 (mmm) REVERT: A 3479 ARG cc_start: 0.9397 (tpp-160) cc_final: 0.9136 (mmm160) REVERT: A 3731 MET cc_start: 0.8825 (tmm) cc_final: 0.8127 (tmm) REVERT: A 3735 MET cc_start: 0.9001 (ptt) cc_final: 0.8592 (ptt) REVERT: A 3819 MET cc_start: 0.9287 (ptp) cc_final: 0.8942 (ptp) REVERT: A 4238 MET cc_start: 0.8235 (pmm) cc_final: 0.7586 (pmm) REVERT: A 4341 LYS cc_start: 0.9301 (mppt) cc_final: 0.8899 (tptp) REVERT: A 4421 MET cc_start: 0.6072 (mmp) cc_final: 0.5832 (mmm) REVERT: A 4429 MET cc_start: 0.2037 (mmt) cc_final: 0.1517 (mmt) REVERT: A 4694 TYR cc_start: 0.9457 (t80) cc_final: 0.8932 (t80) REVERT: A 4695 LEU cc_start: 0.9441 (mm) cc_final: 0.9174 (mm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2155 time to fit residues: 100.5441 Evaluate side-chains 212 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 186 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 437 optimal weight: 0.0770 chunk 268 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 303 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 500 GLN A 541 HIS ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2947 ASN ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4742 GLN ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.046373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.034505 restraints weight = 413413.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.035493 restraints weight = 292954.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.036144 restraints weight = 225714.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.036413 restraints weight = 186764.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.036921 restraints weight = 166883.938| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37635 Z= 0.124 Angle : 0.651 12.968 50921 Z= 0.323 Chirality : 0.043 0.258 5726 Planarity : 0.004 0.066 6505 Dihedral : 5.815 88.562 5022 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.43 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.66 (0.13), residues: 4552 helix: 0.59 (0.10), residues: 2527 sheet: -1.13 (0.29), residues: 298 loop : -1.84 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1326 TYR 0.021 0.001 TYR A1854 PHE 0.042 0.001 PHE A4018 TRP 0.014 0.001 TRP A 912 HIS 0.008 0.001 HIS A2491 Details of bonding type rmsd covalent geometry : bond 0.00269 (37623) covalent geometry : angle 0.65015 (50908) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.10079 ( 4) hydrogen bonds : bond 0.03333 ( 1860) hydrogen bonds : angle 4.57392 ( 5430) metal coordination : bond 0.00345 ( 8) metal coordination : angle 2.70918 ( 9) Misc. bond : bond 0.00184 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.497 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: A 664 TRP cc_start: 0.8898 (p-90) cc_final: 0.7803 (p-90) REVERT: A 721 MET cc_start: 0.8798 (mmp) cc_final: 0.8565 (mmm) REVERT: A 867 GLU cc_start: 0.9516 (mp0) cc_final: 0.9308 (mp0) REVERT: A 868 ASP cc_start: 0.8689 (m-30) cc_final: 0.8466 (m-30) REVERT: A 903 LEU cc_start: 0.7454 (mt) cc_final: 0.7050 (tp) REVERT: A 915 LEU cc_start: 0.9539 (pp) cc_final: 0.9144 (mp) REVERT: A 973 ILE cc_start: 0.8435 (pt) cc_final: 0.8201 (tt) REVERT: A 1442 MET cc_start: 0.7485 (tpt) cc_final: 0.5904 (mmm) REVERT: A 1547 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8502 (mt-10) REVERT: A 1596 MET cc_start: 0.9036 (mmm) cc_final: 0.8684 (mpp) REVERT: A 1615 MET cc_start: 0.8882 (mpp) cc_final: 0.8059 (mpp) REVERT: A 1620 GLU cc_start: 0.7316 (pm20) cc_final: 0.7074 (pm20) REVERT: A 1737 MET cc_start: 0.9538 (mpp) cc_final: 0.9172 (mpp) REVERT: A 1811 MET cc_start: 0.7986 (mtp) cc_final: 0.7697 (mtp) REVERT: A 2042 MET cc_start: 0.8107 (tmm) cc_final: 0.7694 (tmm) REVERT: A 2102 MET cc_start: -0.1793 (ppp) cc_final: -0.2199 (ptp) REVERT: A 2274 MET cc_start: 0.7423 (tpt) cc_final: 0.7006 (tpt) REVERT: A 2276 MET cc_start: 0.5377 (mmp) cc_final: 0.4783 (mmp) REVERT: A 2307 MET cc_start: 0.5156 (ppp) cc_final: 0.3454 (ppp) REVERT: A 2361 MET cc_start: 0.9515 (mtm) cc_final: 0.9026 (mtt) REVERT: A 2648 MET cc_start: 0.5524 (mmp) cc_final: 0.5122 (mmt) REVERT: A 2715 MET cc_start: 0.9148 (mmp) cc_final: 0.8904 (mmm) REVERT: A 2716 MET cc_start: 0.9528 (mtt) cc_final: 0.9299 (mtp) REVERT: A 2747 MET cc_start: 0.9669 (ttm) cc_final: 0.9179 (ttm) REVERT: A 2917 TYR cc_start: 0.8565 (t80) cc_final: 0.8304 (t80) REVERT: A 3382 MET cc_start: 0.7066 (mmp) cc_final: 0.6362 (mmm) REVERT: A 3479 ARG cc_start: 0.9318 (tpp-160) cc_final: 0.9034 (mmm160) REVERT: A 3731 MET cc_start: 0.8739 (tmm) cc_final: 0.7952 (tmm) REVERT: A 3735 MET cc_start: 0.8940 (ptt) cc_final: 0.8450 (ptt) REVERT: A 3806 MET cc_start: 0.8904 (tmm) cc_final: 0.8332 (tmm) REVERT: A 3814 MET cc_start: 0.9166 (mpp) cc_final: 0.8908 (mpp) REVERT: A 3819 MET cc_start: 0.9261 (ptp) cc_final: 0.8873 (ptp) REVERT: A 3981 MET cc_start: 0.6686 (ppp) cc_final: 0.6458 (ppp) REVERT: A 4238 MET cc_start: 0.8117 (pmm) cc_final: 0.7377 (pmm) REVERT: A 4341 LYS cc_start: 0.9229 (mppt) cc_final: 0.8823 (tptp) REVERT: A 4421 MET cc_start: 0.5872 (mmp) cc_final: 0.5635 (mmm) REVERT: A 4429 MET cc_start: 0.1835 (mmt) cc_final: 0.1284 (mmt) REVERT: A 4694 TYR cc_start: 0.9426 (t80) cc_final: 0.8877 (t80) REVERT: A 4695 LEU cc_start: 0.9432 (mm) cc_final: 0.9128 (mm) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2346 time to fit residues: 109.9843 Evaluate side-chains 217 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 444 optimal weight: 0.0270 chunk 426 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 446 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 358 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 overall best weight: 6.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1968 HIS ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2435 ASN ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 GLN ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4133 HIS ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4696 GLN ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.043245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.032014 restraints weight = 433009.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.032854 restraints weight = 307848.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.033437 restraints weight = 236002.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.033896 restraints weight = 194702.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034279 restraints weight = 167728.374| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 37635 Z= 0.268 Angle : 0.787 14.240 50921 Z= 0.404 Chirality : 0.046 0.302 5726 Planarity : 0.005 0.055 6505 Dihedral : 6.104 75.037 5022 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.16 (0.12), residues: 4552 helix: 0.14 (0.10), residues: 2562 sheet: -1.22 (0.29), residues: 285 loop : -2.06 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1326 TYR 0.025 0.002 TYR A3851 PHE 0.045 0.003 PHE A4018 TRP 0.025 0.002 TRP A3611 HIS 0.010 0.002 HIS A3882 Details of bonding type rmsd covalent geometry : bond 0.00556 (37623) covalent geometry : angle 0.78521 (50908) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.69060 ( 4) hydrogen bonds : bond 0.04205 ( 1860) hydrogen bonds : angle 5.01872 ( 5430) metal coordination : bond 0.00532 ( 8) metal coordination : angle 3.35721 ( 9) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8891 (mmp) cc_final: 0.8527 (mmm) REVERT: A 903 LEU cc_start: 0.7570 (mt) cc_final: 0.7117 (tp) REVERT: A 973 ILE cc_start: 0.8571 (pt) cc_final: 0.8352 (mt) REVERT: A 1442 MET cc_start: 0.7826 (tpt) cc_final: 0.6204 (mmm) REVERT: A 1550 GLU cc_start: 0.9379 (pt0) cc_final: 0.9130 (pp20) REVERT: A 1551 LEU cc_start: 0.9825 (tt) cc_final: 0.9565 (tp) REVERT: A 1596 MET cc_start: 0.9107 (mmm) cc_final: 0.8468 (mpp) REVERT: A 1615 MET cc_start: 0.9002 (mpp) cc_final: 0.8258 (mpp) REVERT: A 1737 MET cc_start: 0.9553 (mpp) cc_final: 0.9187 (mpp) REVERT: A 1751 MET cc_start: 0.8506 (tpp) cc_final: 0.8095 (tmm) REVERT: A 1811 MET cc_start: 0.8064 (mtp) cc_final: 0.7802 (mtp) REVERT: A 1857 LEU cc_start: 0.8672 (mt) cc_final: 0.8466 (mm) REVERT: A 2042 MET cc_start: 0.8467 (tmm) cc_final: 0.8071 (tmm) REVERT: A 2102 MET cc_start: -0.1720 (ppp) cc_final: -0.1945 (ppp) REVERT: A 2276 MET cc_start: 0.6008 (mmp) cc_final: 0.5474 (mmp) REVERT: A 2307 MET cc_start: 0.6186 (ppp) cc_final: 0.4857 (ppp) REVERT: A 2361 MET cc_start: 0.9549 (mtm) cc_final: 0.9055 (mtt) REVERT: A 2648 MET cc_start: 0.5835 (mmp) cc_final: 0.5065 (mmt) REVERT: A 2715 MET cc_start: 0.9278 (mmp) cc_final: 0.9004 (mmm) REVERT: A 2716 MET cc_start: 0.9578 (mtt) cc_final: 0.9358 (mtp) REVERT: A 2747 MET cc_start: 0.9731 (ttm) cc_final: 0.9336 (ttm) REVERT: A 3019 PHE cc_start: 0.9438 (m-80) cc_final: 0.9143 (m-80) REVERT: A 3068 TYR cc_start: 0.8202 (p90) cc_final: 0.7931 (p90) REVERT: A 3382 MET cc_start: 0.7259 (mmp) cc_final: 0.6608 (mmm) REVERT: A 3425 LEU cc_start: 0.9598 (tp) cc_final: 0.9380 (mt) REVERT: A 3529 MET cc_start: 0.8959 (mpp) cc_final: 0.8565 (mpp) REVERT: A 3731 MET cc_start: 0.8877 (tmm) cc_final: 0.8109 (tmm) REVERT: A 3735 MET cc_start: 0.9018 (ptt) cc_final: 0.8564 (ptt) REVERT: A 3819 MET cc_start: 0.9363 (ptp) cc_final: 0.8952 (ptp) REVERT: A 3981 MET cc_start: 0.6443 (ppp) cc_final: 0.6172 (ppp) REVERT: A 4238 MET cc_start: 0.8266 (pmm) cc_final: 0.7585 (pmm) REVERT: A 4341 LYS cc_start: 0.9343 (mppt) cc_final: 0.8929 (tptp) REVERT: A 4421 MET cc_start: 0.6793 (mmp) cc_final: 0.6331 (mmm) REVERT: A 4429 MET cc_start: 0.2302 (mmt) cc_final: 0.1753 (mmt) REVERT: A 4694 TYR cc_start: 0.9480 (t80) cc_final: 0.8932 (t80) REVERT: A 4695 LEU cc_start: 0.9448 (mm) cc_final: 0.9112 (mm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2271 time to fit residues: 97.8608 Evaluate side-chains 190 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 281 optimal weight: 0.8980 chunk 417 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 347 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 350 optimal weight: 5.9990 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 392 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2435 ASN ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4252 GLN ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5096 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.044709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.033160 restraints weight = 416276.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.034058 restraints weight = 291960.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.034770 restraints weight = 225082.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.035243 restraints weight = 184693.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.035592 restraints weight = 159095.566| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37635 Z= 0.143 Angle : 0.691 15.407 50921 Z= 0.344 Chirality : 0.044 0.292 5726 Planarity : 0.004 0.058 6505 Dihedral : 5.933 75.375 5022 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.97 (0.12), residues: 4552 helix: 0.29 (0.10), residues: 2560 sheet: -1.08 (0.29), residues: 285 loop : -1.96 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A4330 TYR 0.022 0.002 TYR A3206 PHE 0.042 0.002 PHE A4018 TRP 0.022 0.002 TRP A 884 HIS 0.009 0.001 HIS A2491 Details of bonding type rmsd covalent geometry : bond 0.00315 (37623) covalent geometry : angle 0.68937 (50908) SS BOND : bond 0.00120 ( 2) SS BOND : angle 1.33600 ( 4) hydrogen bonds : bond 0.03529 ( 1860) hydrogen bonds : angle 4.77427 ( 5430) metal coordination : bond 0.00356 ( 8) metal coordination : angle 3.53069 ( 9) Misc. bond : bond 0.00136 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8873 (mmp) cc_final: 0.8483 (mmm) REVERT: A 868 ASP cc_start: 0.8703 (m-30) cc_final: 0.8467 (m-30) REVERT: A 878 LEU cc_start: 0.9153 (pp) cc_final: 0.8678 (mp) REVERT: A 903 LEU cc_start: 0.7652 (mt) cc_final: 0.7229 (tp) REVERT: A 915 LEU cc_start: 0.9554 (pp) cc_final: 0.9210 (mp) REVERT: A 973 ILE cc_start: 0.8522 (pt) cc_final: 0.8313 (tt) REVERT: A 1442 MET cc_start: 0.7640 (tpt) cc_final: 0.6976 (tpt) REVERT: A 1550 GLU cc_start: 0.9271 (pt0) cc_final: 0.9037 (pp20) REVERT: A 1551 LEU cc_start: 0.9809 (tt) cc_final: 0.9516 (tp) REVERT: A 1615 MET cc_start: 0.9039 (mpp) cc_final: 0.8323 (mpp) REVERT: A 1737 MET cc_start: 0.9538 (mpp) cc_final: 0.9136 (mpp) REVERT: A 1751 MET cc_start: 0.8416 (tpp) cc_final: 0.7900 (tmm) REVERT: A 1811 MET cc_start: 0.8073 (mtp) cc_final: 0.7810 (mtp) REVERT: A 2042 MET cc_start: 0.8278 (tmm) cc_final: 0.7885 (tmm) REVERT: A 2102 MET cc_start: -0.1781 (ppp) cc_final: -0.2003 (ppp) REVERT: A 2276 MET cc_start: 0.5878 (mmp) cc_final: 0.4950 (mmp) REVERT: A 2307 MET cc_start: 0.5991 (ppp) cc_final: 0.4565 (ppp) REVERT: A 2361 MET cc_start: 0.9504 (mtm) cc_final: 0.9023 (mtt) REVERT: A 2648 MET cc_start: 0.5510 (mmp) cc_final: 0.4953 (mmt) REVERT: A 2715 MET cc_start: 0.9183 (mmp) cc_final: 0.8925 (mmm) REVERT: A 2716 MET cc_start: 0.9534 (mtt) cc_final: 0.9306 (mtp) REVERT: A 2747 MET cc_start: 0.9729 (ttm) cc_final: 0.9267 (ttm) REVERT: A 2923 MET cc_start: 0.9449 (ptt) cc_final: 0.8974 (ppp) REVERT: A 3001 TYR cc_start: 0.8441 (m-10) cc_final: 0.8164 (m-80) REVERT: A 3019 PHE cc_start: 0.9355 (m-80) cc_final: 0.9085 (m-80) REVERT: A 3382 MET cc_start: 0.6293 (mmm) cc_final: 0.5673 (mmm) REVERT: A 3731 MET cc_start: 0.8823 (tmm) cc_final: 0.7980 (tmm) REVERT: A 3735 MET cc_start: 0.8960 (ptt) cc_final: 0.8521 (ptt) REVERT: A 3819 MET cc_start: 0.9306 (ptp) cc_final: 0.8881 (ptp) REVERT: A 3981 MET cc_start: 0.6526 (ppp) cc_final: 0.6233 (ppp) REVERT: A 4238 MET cc_start: 0.8132 (pmm) cc_final: 0.7391 (pmm) REVERT: A 4304 MET cc_start: 0.8988 (mmp) cc_final: 0.8784 (mmp) REVERT: A 4341 LYS cc_start: 0.9307 (mppt) cc_final: 0.8889 (tptp) REVERT: A 4364 PHE cc_start: 0.9211 (t80) cc_final: 0.9004 (t80) REVERT: A 4421 MET cc_start: 0.6580 (mmp) cc_final: 0.6134 (mmm) REVERT: A 4535 LEU cc_start: 0.9099 (mm) cc_final: 0.8715 (pp) REVERT: A 4694 TYR cc_start: 0.9458 (t80) cc_final: 0.8854 (t80) REVERT: A 4695 LEU cc_start: 0.9425 (mm) cc_final: 0.9072 (mm) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2264 time to fit residues: 103.9307 Evaluate side-chains 210 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 23 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 428 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 308 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 500 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 GLN ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A4001 HIS ** A4008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4406 GLN ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5096 ASN ** 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 = 0.3537 r_free = 0.3537 target = 0.043604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.032371 restraints weight = 427515.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.033152 restraints weight = 305457.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.033849 restraints weight = 236631.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.034273 restraints weight = 194528.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.034614 restraints weight = 169466.140| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37635 Z= 0.198 Angle : 0.731 14.661 50921 Z= 0.369 Chirality : 0.044 0.316 5726 Planarity : 0.005 0.080 6505 Dihedral : 6.026 80.997 5022 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.92 % Favored : 91.04 % Rotamer: Outliers : 0.02 % Allowed : 0.85 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4552 helix: 0.23 (0.10), residues: 2560 sheet: -1.19 (0.29), residues: 290 loop : -2.01 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 937 TYR 0.018 0.002 TYR A2654 PHE 0.042 0.002 PHE A4018 TRP 0.041 0.002 TRP A 884 HIS 0.009 0.001 HIS A2491 Details of bonding type rmsd covalent geometry : bond 0.00422 (37623) covalent geometry : angle 0.72964 (50908) SS BOND : bond 0.00277 ( 2) SS BOND : angle 2.72726 ( 4) hydrogen bonds : bond 0.03773 ( 1860) hydrogen bonds : angle 4.91657 ( 5430) metal coordination : bond 0.00475 ( 8) metal coordination : angle 3.14176 ( 9) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8942 (mmp) cc_final: 0.8566 (mmm) REVERT: A 772 LEU cc_start: 0.8702 (tt) cc_final: 0.8489 (tt) REVERT: A 903 LEU cc_start: 0.7748 (mt) cc_final: 0.7322 (tp) REVERT: A 973 ILE cc_start: 0.8562 (pt) cc_final: 0.8339 (mt) REVERT: A 1442 MET cc_start: 0.7704 (tpt) cc_final: 0.6853 (tpt) REVERT: A 1470 ASP cc_start: 0.9154 (t70) cc_final: 0.8945 (t0) REVERT: A 1550 GLU cc_start: 0.9319 (pt0) cc_final: 0.9097 (pp20) REVERT: A 1551 LEU cc_start: 0.9817 (tt) cc_final: 0.9321 (pp) REVERT: A 1615 MET cc_start: 0.9018 (mpp) cc_final: 0.8309 (mpp) REVERT: A 1737 MET cc_start: 0.9538 (mpp) cc_final: 0.9136 (mpp) REVERT: A 1751 MET cc_start: 0.8470 (tpp) cc_final: 0.8039 (tmm) REVERT: A 1811 MET cc_start: 0.8089 (mtp) cc_final: 0.7843 (mtp) REVERT: A 2042 MET cc_start: 0.8445 (tmm) cc_final: 0.8046 (tmm) REVERT: A 2102 MET cc_start: -0.1906 (ppp) cc_final: -0.2114 (ppp) REVERT: A 2115 MET cc_start: 0.5141 (mpp) cc_final: 0.4713 (mpp) REVERT: A 2276 MET cc_start: 0.6284 (mmp) cc_final: 0.5433 (mmp) REVERT: A 2307 MET cc_start: 0.6301 (ppp) cc_final: 0.5166 (ppp) REVERT: A 2361 MET cc_start: 0.9515 (mtm) cc_final: 0.9018 (mtt) REVERT: A 2648 MET cc_start: 0.5660 (mmp) cc_final: 0.5055 (mmt) REVERT: A 2715 MET cc_start: 0.9265 (mmp) cc_final: 0.8951 (mmm) REVERT: A 2747 MET cc_start: 0.9252 (ttm) cc_final: 0.8854 (tpp) REVERT: A 2923 MET cc_start: 0.9525 (ptt) cc_final: 0.9006 (ppp) REVERT: A 3001 TYR cc_start: 0.8636 (m-10) cc_final: 0.8334 (m-80) REVERT: A 3019 PHE cc_start: 0.9416 (m-80) cc_final: 0.9105 (m-80) REVERT: A 3382 MET cc_start: 0.6228 (mmm) cc_final: 0.5583 (mmt) REVERT: A 3731 MET cc_start: 0.8878 (tmm) cc_final: 0.8101 (tmm) REVERT: A 3733 LEU cc_start: 0.9783 (mt) cc_final: 0.9465 (pp) REVERT: A 3735 MET cc_start: 0.9020 (ptt) cc_final: 0.8591 (ptt) REVERT: A 3814 MET cc_start: 0.9194 (mpp) cc_final: 0.8927 (mpp) REVERT: A 3819 MET cc_start: 0.9282 (ptp) cc_final: 0.8886 (ptp) REVERT: A 3981 MET cc_start: 0.6443 (ppp) cc_final: 0.6155 (ppp) REVERT: A 4238 MET cc_start: 0.8197 (pmm) cc_final: 0.7424 (pmm) REVERT: A 4304 MET cc_start: 0.8939 (mmp) cc_final: 0.8721 (mmp) REVERT: A 4341 LYS cc_start: 0.9339 (mppt) cc_final: 0.8931 (tptp) REVERT: A 4364 PHE cc_start: 0.9190 (t80) cc_final: 0.8978 (t80) REVERT: A 4421 MET cc_start: 0.6744 (mmp) cc_final: 0.6131 (mmm) REVERT: A 4535 LEU cc_start: 0.9087 (mm) cc_final: 0.8695 (pp) REVERT: A 4537 MET cc_start: 0.8543 (ptt) cc_final: 0.8341 (ptp) REVERT: A 4695 LEU cc_start: 0.9443 (mm) cc_final: 0.9242 (mm) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.2129 time to fit residues: 91.9086 Evaluate side-chains 197 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 47 optimal weight: 7.9990 chunk 403 optimal weight: 0.0020 chunk 408 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 412 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 397 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 418 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 GLN ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3561 GLN A4001 HIS A4008 HIS ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5096 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.044107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.032859 restraints weight = 418844.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.033697 restraints weight = 301418.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.034307 restraints weight = 231987.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.034791 restraints weight = 190598.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.035192 restraints weight = 163169.434| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37635 Z= 0.163 Angle : 0.711 15.315 50921 Z= 0.356 Chirality : 0.044 0.378 5726 Planarity : 0.004 0.058 6505 Dihedral : 5.949 81.868 5022 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.17 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.99 (0.12), residues: 4552 helix: 0.27 (0.10), residues: 2567 sheet: -1.17 (0.29), residues: 282 loop : -1.97 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 937 TYR 0.020 0.002 TYR A3206 PHE 0.042 0.002 PHE A4018 TRP 0.030 0.002 TRP A 884 HIS 0.010 0.001 HIS A2491 Details of bonding type rmsd covalent geometry : bond 0.00353 (37623) covalent geometry : angle 0.70886 (50908) SS BOND : bond 0.00114 ( 2) SS BOND : angle 2.60899 ( 4) hydrogen bonds : bond 0.03556 ( 1860) hydrogen bonds : angle 4.87441 ( 5430) metal coordination : bond 0.00435 ( 8) metal coordination : angle 3.47999 ( 9) Misc. bond : bond 0.00118 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9104 Ramachandran restraints generated. 4552 Oldfield, 0 Emsley, 4552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.8967 (mmp) cc_final: 0.8547 (mmm) REVERT: A 903 LEU cc_start: 0.7717 (mt) cc_final: 0.7308 (tp) REVERT: A 973 ILE cc_start: 0.8472 (pt) cc_final: 0.8253 (mt) REVERT: A 1442 MET cc_start: 0.7440 (tpt) cc_final: 0.6706 (tpt) REVERT: A 1470 ASP cc_start: 0.9153 (t70) cc_final: 0.8929 (t0) REVERT: A 1550 GLU cc_start: 0.9281 (pt0) cc_final: 0.9019 (pp20) REVERT: A 1551 LEU cc_start: 0.9811 (tt) cc_final: 0.9493 (tp) REVERT: A 1615 MET cc_start: 0.8984 (mpp) cc_final: 0.8312 (mpp) REVERT: A 1737 MET cc_start: 0.9550 (mpp) cc_final: 0.9164 (mpp) REVERT: A 1751 MET cc_start: 0.8334 (tpp) cc_final: 0.7940 (tmm) REVERT: A 1811 MET cc_start: 0.8092 (mtp) cc_final: 0.7841 (mtp) REVERT: A 2042 MET cc_start: 0.8433 (tmm) cc_final: 0.8184 (tmm) REVERT: A 2115 MET cc_start: 0.5044 (mpp) cc_final: 0.4604 (mpp) REVERT: A 2276 MET cc_start: 0.6620 (mmp) cc_final: 0.5741 (mmp) REVERT: A 2307 MET cc_start: 0.6267 (ppp) cc_final: 0.5113 (ppp) REVERT: A 2361 MET cc_start: 0.9481 (mtm) cc_final: 0.8967 (mtt) REVERT: A 2648 MET cc_start: 0.5461 (mmp) cc_final: 0.4830 (mmt) REVERT: A 2715 MET cc_start: 0.9188 (mmp) cc_final: 0.8879 (mmm) REVERT: A 2716 MET cc_start: 0.9525 (mtt) cc_final: 0.9251 (mtp) REVERT: A 2747 MET cc_start: 0.9233 (ttm) cc_final: 0.8838 (tpp) REVERT: A 2923 MET cc_start: 0.9520 (ptt) cc_final: 0.9064 (ppp) REVERT: A 3001 TYR cc_start: 0.8625 (m-10) cc_final: 0.8344 (m-80) REVERT: A 3019 PHE cc_start: 0.9437 (m-80) cc_final: 0.9103 (m-80) REVERT: A 3382 MET cc_start: 0.5965 (mmm) cc_final: 0.5369 (mmt) REVERT: A 3425 LEU cc_start: 0.9719 (tt) cc_final: 0.9416 (mt) REVERT: A 3731 MET cc_start: 0.8865 (tmm) cc_final: 0.8014 (tmm) REVERT: A 3733 LEU cc_start: 0.9816 (mt) cc_final: 0.9531 (pp) REVERT: A 3735 MET cc_start: 0.9003 (ptt) cc_final: 0.8569 (ptt) REVERT: A 3814 MET cc_start: 0.9212 (mpp) cc_final: 0.8932 (mpp) REVERT: A 3819 MET cc_start: 0.9289 (ptp) cc_final: 0.8885 (ptp) REVERT: A 3981 MET cc_start: 0.6480 (ppp) cc_final: 0.6171 (ppp) REVERT: A 4238 MET cc_start: 0.8146 (pmm) cc_final: 0.7368 (pmm) REVERT: A 4304 MET cc_start: 0.8960 (mmp) cc_final: 0.8730 (mmp) REVERT: A 4341 LYS cc_start: 0.9330 (mppt) cc_final: 0.8936 (tptp) REVERT: A 4364 PHE cc_start: 0.9202 (t80) cc_final: 0.8974 (t80) REVERT: A 4421 MET cc_start: 0.6911 (mmp) cc_final: 0.6360 (mmm) REVERT: A 4535 LEU cc_start: 0.9085 (mm) cc_final: 0.8707 (pp) REVERT: A 4537 MET cc_start: 0.8492 (ptt) cc_final: 0.8285 (ptp) REVERT: A 4695 LEU cc_start: 0.9405 (mm) cc_final: 0.9184 (mm) REVERT: A 4739 LYS cc_start: 0.9436 (pptt) cc_final: 0.9200 (mmtt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2109 time to fit residues: 90.1019 Evaluate side-chains 200 residues out of total 4121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 160 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 455 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 320 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 421 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 overall best weight: 3.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3023 GLN ** A3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3561 GLN A4001 HIS ** A4312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4564 GLN ** A4602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.043864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.032664 restraints weight = 419973.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.033424 restraints weight = 298607.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.034084 restraints weight = 230613.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.034521 restraints weight = 188477.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.034882 restraints weight = 162594.430| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37635 Z= 0.166 Angle : 0.708 14.479 50921 Z= 0.355 Chirality : 0.044 0.366 5726 Planarity : 0.004 0.059 6505 Dihedral : 5.875 84.838 5022 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.57 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.53 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.99 (0.12), residues: 4552 helix: 0.31 (0.10), residues: 2574 sheet: -1.18 (0.29), residues: 282 loop : -2.05 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 508 TYR 0.020 0.002 TYR A1662 PHE 0.043 0.002 PHE A4018 TRP 0.028 0.002 TRP A 884 HIS 0.010 0.001 HIS A2491 Details of bonding type rmsd covalent geometry : bond 0.00358 (37623) covalent geometry : angle 0.70709 (50908) SS BOND : bond 0.00166 ( 2) SS BOND : angle 2.34817 ( 4) hydrogen bonds : bond 0.03544 ( 1860) hydrogen bonds : angle 4.87272 ( 5430) metal coordination : bond 0.00398 ( 8) metal coordination : angle 2.94850 ( 9) Misc. bond : bond 0.00122 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6764.07 seconds wall clock time: 118 minutes 37.44 seconds (7117.44 seconds total)