Starting phenix.real_space_refine on Fri Mar 6 04:07:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.map" model { file = "/net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi6_23841/03_2026/7mi6_23841.cif" } resolution = 3.9 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 Anisotropic ADP refinement not supported. Converting 9873 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Br 2 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 91 5.16 5 Cl 2 4.86 5 C 12620 2.51 5 N 3247 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19653 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2419, 19561 Classifications: {'peptide': 2419} Link IDs: {'PTRANS': 66, 'TRANS': 2352} Chain breaks: 3 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.92, per 1000 atoms: 0.25 Number of scatterers: 19653 At special positions: 0 Unit cell: (118.622, 155.4, 154.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Br 2 34.99 Cl 2 17.00 S 91 16.00 P 3 15.00 Mg 1 11.99 O 3687 8.00 N 3247 7.00 C 12620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 15 sheets defined 64.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1365 through 1379 removed outlier: 4.178A pdb=" N LYS A1369 " --> pdb=" O PHE A1365 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1415 Processing helix chain 'A' and resid 1416 through 1418 No H-bonds generated for 'chain 'A' and resid 1416 through 1418' Processing helix chain 'A' and resid 1425 through 1460 removed outlier: 3.760A pdb=" N LYS A1437 " --> pdb=" O SER A1433 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A1444 " --> pdb=" O GLU A1440 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A1458 " --> pdb=" O ASP A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1469 Processing helix chain 'A' and resid 1469 through 1492 removed outlier: 3.695A pdb=" N THR A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A1478 " --> pdb=" O SER A1474 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1502 Processing helix chain 'A' and resid 1505 through 1534 removed outlier: 3.605A pdb=" N SER A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1525 " --> pdb=" O SER A1521 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A1527 " --> pdb=" O LEU A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1541 removed outlier: 4.019A pdb=" N LEU A1540 " --> pdb=" O ARG A1536 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A1541 " --> pdb=" O PHE A1537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1536 through 1541' Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1557 through 1567 removed outlier: 4.380A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.701A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.514A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1667 removed outlier: 3.749A pdb=" N LYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1689 removed outlier: 3.641A pdb=" N TYR A1672 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.973A pdb=" N LYS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS A1697 " --> pdb=" O ASN A1693 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.904A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1745 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.775A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 removed outlier: 3.529A pdb=" N LEU A1813 " --> pdb=" O PHE A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1842 Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 removed outlier: 3.569A pdb=" N LYS A1913 " --> pdb=" O PRO A1909 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1909 through 1914' Processing helix chain 'A' and resid 1926 through 1938 Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1985 Proline residue: A1982 - end of helix removed outlier: 4.153A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2006 removed outlier: 3.783A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A2003 " --> pdb=" O LYS A1999 " (cutoff:3.500A) Proline residue: A2004 - end of helix Processing helix chain 'A' and resid 2007 through 2022 removed outlier: 4.052A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A2013 " --> pdb=" O THR A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2105 through 2109 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2159 through 2165 removed outlier: 3.743A pdb=" N VAL A2163 " --> pdb=" O ASP A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 4.080A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2241 removed outlier: 3.834A pdb=" N ALA A2236 " --> pdb=" O LYS A2232 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A2239 " --> pdb=" O GLU A2235 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A2240 " --> pdb=" O ALA A2236 " (cutoff:3.500A) Processing helix chain 'A' and resid 2242 through 2258 removed outlier: 4.187A pdb=" N LYS A2248 " --> pdb=" O PHE A2244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2268 removed outlier: 4.022A pdb=" N THR A2263 " --> pdb=" O MET A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.735A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2303 removed outlier: 3.779A pdb=" N GLN A2303 " --> pdb=" O ARG A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2332 through 2346 removed outlier: 3.788A pdb=" N GLN A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A2341 " --> pdb=" O ALA A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2435 removed outlier: 3.890A pdb=" N MET A2428 " --> pdb=" O LYS A2424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A2435 " --> pdb=" O ALA A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2462 removed outlier: 4.069A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS A2461 " --> pdb=" O ALA A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2564 through 2579 Processing helix chain 'A' and resid 2580 through 2587 Proline residue: A2583 - end of helix removed outlier: 4.658A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2619 through 2635 Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2658 through 2660 No H-bonds generated for 'chain 'A' and resid 2658 through 2660' Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.749A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2778 removed outlier: 3.594A pdb=" N ARG A2771 " --> pdb=" O THR A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.980A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2845 removed outlier: 3.832A pdb=" N GLN A2845 " --> pdb=" O ASP A2842 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 Processing helix chain 'A' and resid 2869 through 2884 removed outlier: 3.654A pdb=" N LEU A2873 " --> pdb=" O THR A2869 " (cutoff:3.500A) Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2910 Processing helix chain 'A' and resid 2921 through 2936 removed outlier: 4.176A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE A2936 " --> pdb=" O MET A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2941 through 2945 removed outlier: 4.125A pdb=" N VAL A2945 " --> pdb=" O ASP A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2980 Processing helix chain 'A' and resid 2989 through 3022 removed outlier: 3.655A pdb=" N VAL A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A3001 " --> pdb=" O ARG A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3306 through 3334 removed outlier: 3.674A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A3325 " --> pdb=" O ILE A3321 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A3326 " --> pdb=" O GLY A3322 " (cutoff:3.500A) Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.677A pdb=" N LEU A3352 " --> pdb=" O ILE A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3382 removed outlier: 3.968A pdb=" N LEU A3380 " --> pdb=" O LYS A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3400 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 4.181A pdb=" N SER A3419 " --> pdb=" O ILE A3415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.576A pdb=" N ILE A3466 " --> pdb=" O ILE A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3523 through 3538 removed outlier: 4.517A pdb=" N PHE A3530 " --> pdb=" O GLU A3526 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A3531 " --> pdb=" O THR A3527 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3568 removed outlier: 3.650A pdb=" N GLU A3546 " --> pdb=" O GLN A3542 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A3549 " --> pdb=" O ARG A3545 " (cutoff:3.500A) Processing helix chain 'A' and resid 3587 through 3614 removed outlier: 3.840A pdb=" N LEU A3601 " --> pdb=" O ILE A3597 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER A3604 " --> pdb=" O LYS A3600 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A3607 " --> pdb=" O GLU A3603 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A3608 " --> pdb=" O SER A3604 " (cutoff:3.500A) Proline residue: A3609 - end of helix removed outlier: 3.661A pdb=" N LEU A3614 " --> pdb=" O GLN A3610 " (cutoff:3.500A) Processing helix chain 'A' and resid 3615 through 3639 removed outlier: 3.636A pdb=" N HIS A3624 " --> pdb=" O ILE A3620 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3655 removed outlier: 3.517A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A3655 " --> pdb=" O SER A3651 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 removed outlier: 3.884A pdb=" N TRP A3676 " --> pdb=" O ASP A3672 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A3687 " --> pdb=" O TYR A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.491A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A3710 " --> pdb=" O TYR A3706 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3745 through 3753 Processing helix chain 'A' and resid 3756 through 3768 removed outlier: 4.213A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A3767 " --> pdb=" O PHE A3763 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A3768 " --> pdb=" O LYS A3764 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3781 Processing helix chain 'A' and resid 3796 through 3808 removed outlier: 3.528A pdb=" N GLU A3802 " --> pdb=" O PHE A3798 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 4.349A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3854 removed outlier: 3.641A pdb=" N THR A3853 " --> pdb=" O SER A3849 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3861 removed outlier: 4.483A pdb=" N GLU A3861 " --> pdb=" O LYS A3857 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3870 removed outlier: 4.374A pdb=" N LYS A3870 " --> pdb=" O GLU A3866 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3902 through 3913 removed outlier: 3.535A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3913 through 3918 removed outlier: 4.589A pdb=" N THR A3917 " --> pdb=" O SER A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3922 through 3944 removed outlier: 3.782A pdb=" N VAL A3926 " --> pdb=" O GLY A3922 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A3927 " --> pdb=" O VAL A3923 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 4.092A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 removed outlier: 4.125A pdb=" N ARG A3986 " --> pdb=" O TRP A3982 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A3987 " --> pdb=" O ALA A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 3.564A pdb=" N HIS A4013 " --> pdb=" O LYS A4009 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4092 removed outlier: 3.800A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A4092 " --> pdb=" O LEU A4088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1385 through 1387 Processing sheet with id=AA2, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.832A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N PHE A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N GLU A1594 " --> pdb=" O PHE A1578 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1818 through 1821 removed outlier: 3.792A pdb=" N ASP A1848 " --> pdb=" O PHE A1820 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A1793 " --> pdb=" O ARG A1917 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA6, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.188A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2358 through 2362 removed outlier: 3.965A pdb=" N SER A2367 " --> pdb=" O ALA A2362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.528A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2465 through 2467 removed outlier: 12.542A pdb=" N THR A2472 " --> pdb=" O GLU A2527 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU A2527 " --> pdb=" O THR A2472 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A2525 " --> pdb=" O LEU A2474 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.770A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.609A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3471 through 3472 removed outlier: 3.650A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3812 through 3815 removed outlier: 3.672A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.29: 3270 1.29 - 1.45: 5710 1.45 - 1.61: 10933 1.61 - 1.78: 27 1.78 - 1.94: 122 Bond restraints: 20062 Sorted by residual: bond pdb=" C14 ZG7 A4201 " pdb=" N15 ZG7 A4201 " ideal model delta sigma weight residual 1.328 1.527 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C14 ZG7 A4202 " pdb=" N15 ZG7 A4202 " ideal model delta sigma weight residual 1.328 1.509 -0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C26 ZG7 A4201 " pdb=" O27 ZG7 A4201 " ideal model delta sigma weight residual 1.305 1.154 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C4 ATP A4203 " pdb=" C5 ATP A4203 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C16 ZG7 A4201 " pdb=" N15 ZG7 A4201 " ideal model delta sigma weight residual 1.312 1.444 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 20057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 26588 4.42 - 8.84: 484 8.84 - 13.27: 52 13.27 - 17.69: 10 17.69 - 22.11: 2 Bond angle restraints: 27136 Sorted by residual: angle pdb=" PA ATP A4203 " pdb=" O3A ATP A4203 " pdb=" PB ATP A4203 " ideal model delta sigma weight residual 136.83 121.05 15.78 1.00e+00 1.00e+00 2.49e+02 angle pdb=" PB ATP A4203 " pdb=" O3B ATP A4203 " pdb=" PG ATP A4203 " ideal model delta sigma weight residual 139.87 128.76 11.11 1.00e+00 1.00e+00 1.23e+02 angle pdb=" C5 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N3 ATP A4203 " ideal model delta sigma weight residual 126.80 118.15 8.65 1.00e+00 1.00e+00 7.49e+01 angle pdb=" N3 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N9 ATP A4203 " ideal model delta sigma weight residual 127.04 136.74 -9.70 1.15e+00 7.59e-01 7.13e+01 angle pdb=" O1G ATP A4203 " pdb=" PG ATP A4203 " pdb=" O3B ATP A4203 " ideal model delta sigma weight residual 110.47 98.96 11.51 1.64e+00 3.70e-01 4.90e+01 ... (remaining 27131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11158 17.98 - 35.96: 683 35.96 - 53.94: 148 53.94 - 71.91: 49 71.91 - 89.89: 28 Dihedral angle restraints: 12066 sinusoidal: 4964 harmonic: 7102 Sorted by residual: dihedral pdb=" CA ASP A2105 " pdb=" C ASP A2105 " pdb=" N THR A2106 " pdb=" CA THR A2106 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLN A2639 " pdb=" C GLN A2639 " pdb=" N THR A2640 " pdb=" CA THR A2640 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" N VAL A3615 " pdb=" C VAL A3615 " pdb=" CA VAL A3615 " pdb=" CB VAL A3615 " ideal model delta harmonic sigma weight residual 123.40 135.08 -11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 12063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2172 0.076 - 0.153: 736 0.153 - 0.229: 129 0.229 - 0.305: 18 0.305 - 0.382: 10 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CB ILE A2141 " pdb=" CA ILE A2141 " pdb=" CG1 ILE A2141 " pdb=" CG2 ILE A2141 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE A2943 " pdb=" N PHE A2943 " pdb=" C PHE A2943 " pdb=" CB PHE A2943 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB VAL A2984 " pdb=" CA VAL A2984 " pdb=" CG1 VAL A2984 " pdb=" CG2 VAL A2984 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3062 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 ZG7 A4201 " -0.017 2.00e-02 2.50e+03 4.17e-02 6.08e+01 pdb=" C11 ZG7 A4201 " 0.092 2.00e-02 2.50e+03 pdb=" C14 ZG7 A4201 " -0.011 2.00e-02 2.50e+03 pdb=" C16 ZG7 A4201 " -0.021 2.00e-02 2.50e+03 pdb=" C17 ZG7 A4201 " -0.030 2.00e-02 2.50e+03 pdb=" C26 ZG7 A4201 " 0.006 2.00e-02 2.50e+03 pdb=" C28 ZG7 A4201 " -0.031 2.00e-02 2.50e+03 pdb=" C29 ZG7 A4201 " 0.006 2.00e-02 2.50e+03 pdb=" N12 ZG7 A4201 " -0.007 2.00e-02 2.50e+03 pdb=" N13 ZG7 A4201 " -0.049 2.00e-02 2.50e+03 pdb=" N15 ZG7 A4201 " -0.013 2.00e-02 2.50e+03 pdb=" N30 ZG7 A4201 " 0.021 2.00e-02 2.50e+03 pdb=" O18 ZG7 A4201 " 0.093 2.00e-02 2.50e+03 pdb=" O27 ZG7 A4201 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2916 " -0.027 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP A2916 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A2916 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A2916 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A2916 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A2916 " 0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP A2916 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2916 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2916 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A2916 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A2857 " -0.028 2.00e-02 2.50e+03 5.61e-02 3.14e+01 pdb=" C ARG A2857 " 0.097 2.00e-02 2.50e+03 pdb=" O ARG A2857 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN A2858 " -0.033 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 216 2.60 - 3.18: 17670 3.18 - 3.75: 30898 3.75 - 4.33: 41433 4.33 - 4.90: 67703 Nonbonded interactions: 157920 Sorted by model distance: nonbonded pdb=" O3G ATP A4203 " pdb="MG MG A4204 " model vdw 2.027 2.170 nonbonded pdb=" O1B ATP A4203 " pdb="MG MG A4204 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4204 " model vdw 2.079 2.170 nonbonded pdb=" O ARG A3445 " pdb=" OG SER A3489 " model vdw 2.122 3.040 nonbonded pdb=" O ASP A3531 " pdb=" OG1 THR A3535 " model vdw 2.195 3.040 ... (remaining 157915 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=0.50 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.280 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.012 0.199 20062 Z= 0.568 Angle : 1.493 22.111 27136 Z= 0.823 Chirality : 0.078 0.382 3065 Planarity : 0.009 0.056 3416 Dihedral : 13.680 89.891 7458 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.27 % Favored : 94.32 % Rotamer: Outliers : 1.32 % Allowed : 4.99 % Favored : 93.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 2411 helix: -1.13 (0.12), residues: 1373 sheet: -1.33 (0.35), residues: 194 loop : -1.99 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG A2830 TYR 0.039 0.005 TYR A2356 PHE 0.084 0.005 PHE A3446 TRP 0.085 0.006 TRP A2916 HIS 0.043 0.004 HIS A1554 Details of bonding type rmsd covalent geometry : bond 0.01233 (20062) covalent geometry : angle 1.49311 (27136) hydrogen bonds : bond 0.13714 ( 1102) hydrogen bonds : angle 6.59453 ( 3225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 568 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1409 LEU cc_start: 0.9479 (mt) cc_final: 0.9226 (mt) REVERT: A 1466 GLN cc_start: 0.8711 (pt0) cc_final: 0.8479 (pt0) REVERT: A 1495 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 1509 LEU cc_start: 0.8845 (mt) cc_final: 0.8419 (mt) REVERT: A 1510 LYS cc_start: 0.8938 (mttp) cc_final: 0.8736 (tppt) REVERT: A 1650 LEU cc_start: 0.9242 (tp) cc_final: 0.9007 (tt) REVERT: A 1848 ASP cc_start: 0.8370 (t0) cc_final: 0.8088 (p0) REVERT: A 1919 PHE cc_start: 0.8172 (t80) cc_final: 0.6388 (t80) REVERT: A 2091 MET cc_start: 0.8010 (mtt) cc_final: 0.7364 (mpp) REVERT: A 2169 VAL cc_start: 0.8901 (t) cc_final: 0.8646 (m) REVERT: A 2171 ASP cc_start: 0.8850 (m-30) cc_final: 0.8600 (m-30) REVERT: A 2190 PHE cc_start: 0.7149 (t80) cc_final: 0.6820 (t80) REVERT: A 2213 LEU cc_start: 0.8411 (tp) cc_final: 0.7988 (mp) REVERT: A 2225 LYS cc_start: 0.8684 (tttt) cc_final: 0.8378 (tttt) REVERT: A 2317 LEU cc_start: 0.9591 (mt) cc_final: 0.9391 (tt) REVERT: A 2805 ASP cc_start: 0.8182 (m-30) cc_final: 0.7979 (m-30) REVERT: A 2914 ILE cc_start: 0.9286 (mt) cc_final: 0.8915 (mt) REVERT: A 2960 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 3012 GLU cc_start: 0.9455 (tm-30) cc_final: 0.8930 (tm-30) REVERT: A 3013 ASN cc_start: 0.9556 (t0) cc_final: 0.9242 (t0) REVERT: A 3014 GLN cc_start: 0.9441 (pt0) cc_final: 0.9111 (pt0) REVERT: A 3015 ARG cc_start: 0.9149 (ttp-170) cc_final: 0.8629 (ttp80) REVERT: A 3016 PHE cc_start: 0.9452 (t80) cc_final: 0.9108 (t80) REVERT: A 3308 ASN cc_start: 0.8599 (t0) cc_final: 0.8083 (t0) REVERT: A 3316 THR cc_start: 0.9786 (m) cc_final: 0.9581 (m) REVERT: A 3538 ASN cc_start: 0.8969 (t0) cc_final: 0.8747 (t0) REVERT: A 3541 MET cc_start: 0.8666 (mmm) cc_final: 0.8040 (mmm) REVERT: A 3621 ILE cc_start: 0.9255 (mt) cc_final: 0.8969 (mt) REVERT: A 3655 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8626 (mtp85) REVERT: A 3681 GLU cc_start: 0.9247 (tp30) cc_final: 0.8615 (tp30) REVERT: A 3700 MET cc_start: 0.8509 (ttm) cc_final: 0.8233 (ttp) REVERT: A 3717 GLU cc_start: 0.9003 (tp30) cc_final: 0.8716 (pp20) REVERT: A 3745 ARG cc_start: 0.7647 (tpt170) cc_final: 0.7297 (mmp-170) REVERT: A 3749 ASP cc_start: 0.8469 (m-30) cc_final: 0.8041 (t0) REVERT: A 3767 PHE cc_start: 0.7846 (m-80) cc_final: 0.7473 (m-80) REVERT: A 3803 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9061 (pp) REVERT: A 3873 MET cc_start: 0.8595 (ttp) cc_final: 0.8303 (ttm) REVERT: A 3952 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8573 (tmtt) outliers start: 29 outliers final: 8 residues processed: 589 average time/residue: 0.1727 time to fit residues: 149.3490 Evaluate side-chains 304 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 293 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1495 THR Chi-restraints excluded: chain A residue 1793 CYS Chi-restraints excluded: chain A residue 2131 THR Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2960 THR Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3803 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1444 ASN A1449 GLN A1757 GLN A1869 GLN A2068 GLN A2304 ASN A2363 ASN ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2500 GLN A2569 GLN A2854 ASN A2931 ASN A3013 ASN A3308 ASN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3561 ASN A3780 ASN A3784 ASN A3948 HIS A3988 HIS A4077 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.090077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068246 restraints weight = 79809.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070171 restraints weight = 44160.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071517 restraints weight = 30560.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072250 restraints weight = 24197.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072899 restraints weight = 21147.538| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20062 Z= 0.203 Angle : 0.741 10.926 27136 Z= 0.389 Chirality : 0.046 0.307 3065 Planarity : 0.005 0.054 3416 Dihedral : 6.898 83.605 2657 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 2.90 % Allowed : 13.84 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2411 helix: 0.79 (0.13), residues: 1378 sheet: -1.00 (0.35), residues: 197 loop : -1.33 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2646 TYR 0.030 0.002 TYR A2674 PHE 0.032 0.002 PHE A1491 TRP 0.025 0.002 TRP A2084 HIS 0.009 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00438 (20062) covalent geometry : angle 0.74121 (27136) hydrogen bonds : bond 0.04847 ( 1102) hydrogen bonds : angle 5.02068 ( 3225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1466 GLN cc_start: 0.8682 (pt0) cc_final: 0.8280 (mt0) REVERT: A 1497 ILE cc_start: 0.9309 (tp) cc_final: 0.9046 (mt) REVERT: A 1510 LYS cc_start: 0.8952 (mttp) cc_final: 0.8729 (tppt) REVERT: A 1655 MET cc_start: 0.8824 (ttm) cc_final: 0.8240 (tmm) REVERT: A 1790 TYR cc_start: 0.8746 (m-80) cc_final: 0.8426 (m-80) REVERT: A 1813 LEU cc_start: 0.9418 (tt) cc_final: 0.9002 (mp) REVERT: A 1919 PHE cc_start: 0.8103 (t80) cc_final: 0.7630 (t80) REVERT: A 1937 MET cc_start: 0.4501 (mmm) cc_final: 0.3615 (mtt) REVERT: A 2118 MET cc_start: 0.8343 (pmm) cc_final: 0.7794 (tpt) REVERT: A 2127 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7693 (t70) REVERT: A 2135 ARG cc_start: 0.8487 (ttm170) cc_final: 0.8188 (ptm160) REVERT: A 2171 ASP cc_start: 0.8801 (m-30) cc_final: 0.8568 (m-30) REVERT: A 2213 LEU cc_start: 0.8327 (tp) cc_final: 0.7985 (mp) REVERT: A 2618 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9067 (t) REVERT: A 2792 LEU cc_start: 0.9208 (mt) cc_final: 0.8390 (mp) REVERT: A 3013 ASN cc_start: 0.9611 (t0) cc_final: 0.9304 (t0) REVERT: A 3014 GLN cc_start: 0.9426 (pt0) cc_final: 0.9138 (pt0) REVERT: A 3330 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.8620 (t80) REVERT: A 3597 ILE cc_start: 0.9114 (mt) cc_final: 0.8803 (mt) REVERT: A 3600 LYS cc_start: 0.8688 (pttm) cc_final: 0.8447 (pttm) REVERT: A 3681 GLU cc_start: 0.9106 (tp30) cc_final: 0.8834 (tp30) REVERT: A 3717 GLU cc_start: 0.9011 (tp30) cc_final: 0.8678 (pp20) REVERT: A 3722 MET cc_start: 0.8897 (mmt) cc_final: 0.8587 (mmt) REVERT: A 3749 ASP cc_start: 0.8504 (m-30) cc_final: 0.8253 (t0) REVERT: A 3816 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8797 (tp) REVERT: A 3910 LEU cc_start: 0.9503 (mp) cc_final: 0.9238 (mp) outliers start: 64 outliers final: 29 residues processed: 379 average time/residue: 0.1557 time to fit residues: 89.5588 Evaluate side-chains 287 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2131 THR Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3479 VAL Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 LEU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 197 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2201 HIS ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068113 restraints weight = 80425.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070113 restraints weight = 44495.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071536 restraints weight = 30546.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072308 restraints weight = 23799.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.072908 restraints weight = 20434.807| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20062 Z= 0.147 Angle : 0.680 13.205 27136 Z= 0.348 Chirality : 0.044 0.278 3065 Planarity : 0.004 0.041 3416 Dihedral : 6.462 86.289 2644 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 2.45 % Allowed : 15.11 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2411 helix: 1.12 (0.14), residues: 1390 sheet: -0.65 (0.36), residues: 192 loop : -1.27 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2646 TYR 0.023 0.002 TYR A1762 PHE 0.017 0.002 PHE A1491 TRP 0.024 0.001 TRP A2084 HIS 0.013 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00321 (20062) covalent geometry : angle 0.68019 (27136) hydrogen bonds : bond 0.04368 ( 1102) hydrogen bonds : angle 4.73065 ( 3225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1497 ILE cc_start: 0.9263 (tp) cc_final: 0.9019 (mt) REVERT: A 1510 LYS cc_start: 0.8965 (mttp) cc_final: 0.8730 (tppt) REVERT: A 1704 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9045 (mt-10) REVERT: A 1762 TYR cc_start: 0.7560 (t80) cc_final: 0.7285 (t80) REVERT: A 1790 TYR cc_start: 0.8741 (m-80) cc_final: 0.8515 (m-80) REVERT: A 1813 LEU cc_start: 0.9418 (tt) cc_final: 0.8988 (mp) REVERT: A 1919 PHE cc_start: 0.8036 (t80) cc_final: 0.7489 (t80) REVERT: A 1921 MET cc_start: 0.8791 (mmm) cc_final: 0.8474 (mmm) REVERT: A 1932 MET cc_start: 0.6207 (mmp) cc_final: 0.5996 (mmp) REVERT: A 1937 MET cc_start: 0.4397 (mmm) cc_final: 0.3497 (mtt) REVERT: A 1992 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6944 (tptt) REVERT: A 2118 MET cc_start: 0.8356 (pmm) cc_final: 0.7838 (tpt) REVERT: A 2135 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8255 (ptm160) REVERT: A 2171 ASP cc_start: 0.8906 (m-30) cc_final: 0.8658 (m-30) REVERT: A 2213 LEU cc_start: 0.8312 (tp) cc_final: 0.7974 (mp) REVERT: A 2225 LYS cc_start: 0.8770 (tttt) cc_final: 0.8439 (tptm) REVERT: A 2365 LYS cc_start: 0.6126 (tttm) cc_final: 0.5630 (ttmm) REVERT: A 2582 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.8993 (m) REVERT: A 2792 LEU cc_start: 0.9201 (mt) cc_final: 0.8617 (mp) REVERT: A 3013 ASN cc_start: 0.9557 (t0) cc_final: 0.9250 (t0) REVERT: A 3015 ARG cc_start: 0.9125 (ttp-170) cc_final: 0.8733 (ttp80) REVERT: A 3311 LYS cc_start: 0.9275 (tmmt) cc_final: 0.9011 (tmmt) REVERT: A 3330 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8617 (t80) REVERT: A 3541 MET cc_start: 0.8824 (mmm) cc_final: 0.8494 (mmm) REVERT: A 3681 GLU cc_start: 0.8989 (tp30) cc_final: 0.8695 (tp30) REVERT: A 3700 MET cc_start: 0.8207 (ttp) cc_final: 0.7886 (tpp) REVERT: A 3717 GLU cc_start: 0.9048 (tp30) cc_final: 0.8673 (pp20) REVERT: A 3745 ARG cc_start: 0.7994 (tpt170) cc_final: 0.7655 (tpp-160) REVERT: A 3816 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8786 (tp) outliers start: 54 outliers final: 24 residues processed: 340 average time/residue: 0.1457 time to fit residues: 76.4889 Evaluate side-chains 288 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2131 THR Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3816 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 170 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1382 GLN A1449 GLN A1629 GLN A1869 GLN A1967 HIS A2173 ASN A2228 HIS ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3399 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 HIS ** A3497 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.088339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066583 restraints weight = 81994.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068499 restraints weight = 45211.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069794 restraints weight = 31005.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070495 restraints weight = 24768.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071107 restraints weight = 21766.507| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.062 20062 Z= 0.190 Angle : 0.674 12.965 27136 Z= 0.347 Chirality : 0.044 0.286 3065 Planarity : 0.004 0.047 3416 Dihedral : 6.411 86.727 2644 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 2.99 % Allowed : 15.97 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2411 helix: 1.23 (0.14), residues: 1392 sheet: -0.45 (0.36), residues: 195 loop : -1.18 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2586 TYR 0.020 0.002 TYR A1762 PHE 0.017 0.002 PHE A2505 TRP 0.021 0.002 TRP A2084 HIS 0.010 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00416 (20062) covalent geometry : angle 0.67395 (27136) hydrogen bonds : bond 0.04249 ( 1102) hydrogen bonds : angle 4.72305 ( 3225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 269 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1408 ASP cc_start: 0.8733 (t70) cc_final: 0.8498 (t70) REVERT: A 1447 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8831 (mp0) REVERT: A 1493 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 1510 LYS cc_start: 0.9000 (mttp) cc_final: 0.8775 (tppt) REVERT: A 1704 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9021 (mt-10) REVERT: A 1762 TYR cc_start: 0.7756 (t80) cc_final: 0.7466 (t80) REVERT: A 1790 TYR cc_start: 0.8801 (m-80) cc_final: 0.8529 (m-80) REVERT: A 1813 LEU cc_start: 0.9431 (tt) cc_final: 0.9021 (mp) REVERT: A 1919 PHE cc_start: 0.8157 (t80) cc_final: 0.7625 (t80) REVERT: A 1921 MET cc_start: 0.8853 (mmm) cc_final: 0.8624 (mmm) REVERT: A 1936 ILE cc_start: 0.8961 (mt) cc_final: 0.8568 (mt) REVERT: A 1937 MET cc_start: 0.4580 (mmm) cc_final: 0.3571 (mtt) REVERT: A 1992 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6959 (tptt) REVERT: A 2091 MET cc_start: 0.7992 (mtm) cc_final: 0.7788 (mtm) REVERT: A 2118 MET cc_start: 0.8619 (pmm) cc_final: 0.8011 (tpt) REVERT: A 2171 ASP cc_start: 0.8920 (m-30) cc_final: 0.8631 (m-30) REVERT: A 2213 LEU cc_start: 0.8442 (tp) cc_final: 0.8051 (mp) REVERT: A 2225 LYS cc_start: 0.8759 (tttt) cc_final: 0.8422 (tptm) REVERT: A 2365 LYS cc_start: 0.6384 (tttm) cc_final: 0.5985 (ttmm) REVERT: A 2792 LEU cc_start: 0.9241 (mt) cc_final: 0.8877 (mp) REVERT: A 2834 LEU cc_start: 0.9518 (tt) cc_final: 0.9277 (tp) REVERT: A 3013 ASN cc_start: 0.9567 (t0) cc_final: 0.9119 (t0) REVERT: A 3015 ARG cc_start: 0.9108 (ttp-170) cc_final: 0.8721 (ttp80) REVERT: A 3313 PHE cc_start: 0.8867 (t80) cc_final: 0.8361 (t80) REVERT: A 3330 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 3369 TYR cc_start: 0.8816 (t80) cc_final: 0.8515 (t80) REVERT: A 3538 ASN cc_start: 0.9097 (t0) cc_final: 0.8423 (p0) REVERT: A 3540 GLU cc_start: 0.9438 (mm-30) cc_final: 0.8653 (pm20) REVERT: A 3541 MET cc_start: 0.8806 (mmm) cc_final: 0.7963 (mmm) REVERT: A 3599 LYS cc_start: 0.9396 (tppt) cc_final: 0.9186 (tppt) REVERT: A 3681 GLU cc_start: 0.9017 (tp30) cc_final: 0.8747 (tp30) REVERT: A 3700 MET cc_start: 0.8226 (ttp) cc_final: 0.7943 (tpp) REVERT: A 3717 GLU cc_start: 0.9113 (tp30) cc_final: 0.8691 (pp20) REVERT: A 3816 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 3910 LEU cc_start: 0.9512 (mp) cc_final: 0.9266 (mp) outliers start: 66 outliers final: 41 residues processed: 316 average time/residue: 0.1419 time to fit residues: 70.3803 Evaluate side-chains 296 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2063 MET Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2466 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 LEU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 197 optimal weight: 0.0870 chunk 141 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 GLN A1869 GLN ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2508 GLN ** A3497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.090295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069359 restraints weight = 80619.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071655 restraints weight = 47923.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073256 restraints weight = 30486.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073510 restraints weight = 23702.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073600 restraints weight = 21373.807| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20062 Z= 0.120 Angle : 0.660 15.064 27136 Z= 0.328 Chirality : 0.042 0.260 3065 Planarity : 0.004 0.103 3416 Dihedral : 6.157 89.690 2643 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 2.36 % Allowed : 17.24 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.17), residues: 2411 helix: 1.42 (0.14), residues: 1393 sheet: -0.24 (0.38), residues: 192 loop : -1.18 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A2000 TYR 0.018 0.001 TYR A1762 PHE 0.017 0.001 PHE A1505 TRP 0.021 0.001 TRP A2084 HIS 0.006 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00253 (20062) covalent geometry : angle 0.66003 (27136) hydrogen bonds : bond 0.03873 ( 1102) hydrogen bonds : angle 4.46930 ( 3225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.805 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 1493 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 1510 LYS cc_start: 0.8978 (mttp) cc_final: 0.8757 (tppt) REVERT: A 1608 LEU cc_start: 0.9424 (mt) cc_final: 0.9221 (mm) REVERT: A 1692 ASP cc_start: 0.7540 (p0) cc_final: 0.7340 (m-30) REVERT: A 1704 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9064 (mt-10) REVERT: A 1762 TYR cc_start: 0.7750 (t80) cc_final: 0.7404 (t80) REVERT: A 1790 TYR cc_start: 0.8722 (m-80) cc_final: 0.7755 (t80) REVERT: A 1813 LEU cc_start: 0.9388 (tt) cc_final: 0.8966 (mp) REVERT: A 1919 PHE cc_start: 0.8045 (t80) cc_final: 0.7593 (t80) REVERT: A 1921 MET cc_start: 0.8758 (mmm) cc_final: 0.8507 (mmm) REVERT: A 1936 ILE cc_start: 0.8982 (mt) cc_final: 0.8578 (mt) REVERT: A 1937 MET cc_start: 0.4760 (mmm) cc_final: 0.3789 (mtt) REVERT: A 2118 MET cc_start: 0.8613 (pmm) cc_final: 0.8018 (tpt) REVERT: A 2171 ASP cc_start: 0.9051 (m-30) cc_final: 0.8737 (m-30) REVERT: A 2213 LEU cc_start: 0.8545 (tp) cc_final: 0.8091 (mp) REVERT: A 2792 LEU cc_start: 0.9186 (mt) cc_final: 0.8811 (mp) REVERT: A 3013 ASN cc_start: 0.9550 (t0) cc_final: 0.9129 (t0) REVERT: A 3015 ARG cc_start: 0.9114 (ttp-170) cc_final: 0.8545 (ttp80) REVERT: A 3313 PHE cc_start: 0.8891 (t80) cc_final: 0.8374 (t80) REVERT: A 3369 TYR cc_start: 0.8738 (t80) cc_final: 0.8406 (t80) REVERT: A 3379 TRP cc_start: 0.9133 (m-10) cc_final: 0.8771 (m-10) REVERT: A 3538 ASN cc_start: 0.9090 (t0) cc_final: 0.8794 (t0) REVERT: A 3541 MET cc_start: 0.8740 (mmm) cc_final: 0.8288 (mmm) REVERT: A 3599 LYS cc_start: 0.9439 (tppt) cc_final: 0.9211 (tppt) REVERT: A 3677 LEU cc_start: 0.9003 (mm) cc_final: 0.8450 (tt) REVERT: A 3717 GLU cc_start: 0.9141 (tp30) cc_final: 0.8683 (pp20) REVERT: A 3748 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.8035 (m100) REVERT: A 3816 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 3875 MET cc_start: 0.7992 (mpp) cc_final: 0.7185 (mpp) REVERT: A 3910 LEU cc_start: 0.9488 (mp) cc_final: 0.9199 (mp) outliers start: 52 outliers final: 28 residues processed: 342 average time/residue: 0.1441 time to fit residues: 77.3302 Evaluate side-chains 284 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2673 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3816 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 87 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 GLN A1869 GLN ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2304 ASN A2340 GLN ** A2430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2521 ASN ** A2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2871 GLN A3648 GLN 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 = 0.086108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064417 restraints weight = 82224.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066284 restraints weight = 47034.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067448 restraints weight = 32975.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068320 restraints weight = 26670.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068961 restraints weight = 23105.697| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20062 Z= 0.272 Angle : 0.752 14.161 27136 Z= 0.386 Chirality : 0.045 0.264 3065 Planarity : 0.004 0.053 3416 Dihedral : 6.401 85.559 2643 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 3.45 % Allowed : 17.38 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2411 helix: 1.17 (0.14), residues: 1391 sheet: -0.20 (0.36), residues: 192 loop : -1.17 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2000 TYR 0.016 0.002 TYR A1762 PHE 0.020 0.002 PHE A2145 TRP 0.020 0.002 TRP A2084 HIS 0.010 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00596 (20062) covalent geometry : angle 0.75201 (27136) hydrogen bonds : bond 0.04462 ( 1102) hydrogen bonds : angle 4.82583 ( 3225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9070 (mt-10) REVERT: A 1762 TYR cc_start: 0.7884 (t80) cc_final: 0.7656 (t80) REVERT: A 1790 TYR cc_start: 0.8808 (m-80) cc_final: 0.8492 (m-80) REVERT: A 1813 LEU cc_start: 0.9383 (tt) cc_final: 0.8985 (mp) REVERT: A 1992 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6912 (tptt) REVERT: A 2118 MET cc_start: 0.8745 (pmm) cc_final: 0.7986 (tpt) REVERT: A 2213 LEU cc_start: 0.8508 (tp) cc_final: 0.8114 (mp) REVERT: A 3013 ASN cc_start: 0.9533 (t0) cc_final: 0.9126 (t0) REVERT: A 3015 ARG cc_start: 0.9073 (ttp-170) cc_final: 0.8686 (ttp80) REVERT: A 3313 PHE cc_start: 0.8904 (t80) cc_final: 0.8403 (t80) REVERT: A 3330 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8636 (t80) REVERT: A 3538 ASN cc_start: 0.9096 (t0) cc_final: 0.8750 (p0) REVERT: A 3540 GLU cc_start: 0.9450 (mm-30) cc_final: 0.8774 (pm20) REVERT: A 3541 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: A 3616 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: A 3648 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8703 (pm20) REVERT: A 3677 LEU cc_start: 0.9109 (mm) cc_final: 0.8562 (tt) REVERT: A 3701 THR cc_start: 0.9540 (m) cc_final: 0.9314 (p) REVERT: A 3717 GLU cc_start: 0.9137 (tp30) cc_final: 0.8625 (pp20) REVERT: A 3722 MET cc_start: 0.8772 (mmm) cc_final: 0.8442 (mmm) outliers start: 76 outliers final: 48 residues processed: 303 average time/residue: 0.1410 time to fit residues: 67.3277 Evaluate side-chains 284 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1544 ASP Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2330 SER Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2673 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3331 GLU Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3616 GLU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3648 GLN Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 3915 PHE Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 GLN A1870 ASN A1965 HIS ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2871 GLN ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.088618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066963 restraints weight = 81210.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068982 restraints weight = 45898.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070272 restraints weight = 31932.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071173 restraints weight = 25495.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071655 restraints weight = 21901.292| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20062 Z= 0.131 Angle : 0.692 16.046 27136 Z= 0.342 Chirality : 0.043 0.236 3065 Planarity : 0.004 0.054 3416 Dihedral : 6.130 88.773 2643 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 2.45 % Allowed : 18.87 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2411 helix: 1.39 (0.14), residues: 1394 sheet: -0.12 (0.37), residues: 195 loop : -1.20 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2000 TYR 0.030 0.001 TYR A3369 PHE 0.022 0.001 PHE A3768 TRP 0.022 0.001 TRP A2084 HIS 0.008 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00291 (20062) covalent geometry : angle 0.69174 (27136) hydrogen bonds : bond 0.03947 ( 1102) hydrogen bonds : angle 4.54743 ( 3225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9022 (mt-10) REVERT: A 1762 TYR cc_start: 0.7825 (t80) cc_final: 0.7573 (t80) REVERT: A 1790 TYR cc_start: 0.8767 (m-80) cc_final: 0.7756 (t80) REVERT: A 1813 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8963 (mp) REVERT: A 1919 PHE cc_start: 0.8088 (t80) cc_final: 0.7477 (t80) REVERT: A 1937 MET cc_start: 0.4830 (mmm) cc_final: 0.3877 (mtt) REVERT: A 2063 MET cc_start: 0.9229 (tpp) cc_final: 0.8910 (tpp) REVERT: A 2213 LEU cc_start: 0.8558 (tp) cc_final: 0.8148 (mp) REVERT: A 2225 LYS cc_start: 0.8750 (tttt) cc_final: 0.8366 (tptm) REVERT: A 2756 MET cc_start: 0.8820 (tpp) cc_final: 0.8308 (ttt) REVERT: A 2792 LEU cc_start: 0.9166 (mt) cc_final: 0.8611 (mp) REVERT: A 3013 ASN cc_start: 0.9524 (t0) cc_final: 0.9125 (t0) REVERT: A 3015 ARG cc_start: 0.9071 (ttp-170) cc_final: 0.8676 (ttp80) REVERT: A 3311 LYS cc_start: 0.9187 (tmmt) cc_final: 0.8902 (tmmt) REVERT: A 3313 PHE cc_start: 0.8941 (t80) cc_final: 0.8432 (t80) REVERT: A 3330 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8628 (t80) REVERT: A 3394 MET cc_start: 0.9047 (tpp) cc_final: 0.8778 (tpp) REVERT: A 3538 ASN cc_start: 0.9097 (t0) cc_final: 0.8451 (p0) REVERT: A 3540 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8645 (pm20) REVERT: A 3541 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: A 3677 LEU cc_start: 0.9020 (mm) cc_final: 0.8519 (tt) REVERT: A 3702 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (mpp) REVERT: A 3717 GLU cc_start: 0.9129 (tp30) cc_final: 0.8588 (pp20) REVERT: A 3722 MET cc_start: 0.8651 (mmm) cc_final: 0.8437 (mmm) REVERT: A 3768 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6314 (m-10) outliers start: 54 outliers final: 37 residues processed: 296 average time/residue: 0.1332 time to fit residues: 63.1882 Evaluate side-chains 284 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1544 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1794 PHE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2673 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3895 VAL Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 GLN ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065150 restraints weight = 81957.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067031 restraints weight = 46882.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068404 restraints weight = 32593.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069275 restraints weight = 25814.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069556 restraints weight = 22194.024| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20062 Z= 0.199 Angle : 0.711 13.939 27136 Z= 0.358 Chirality : 0.044 0.339 3065 Planarity : 0.004 0.045 3416 Dihedral : 6.146 86.724 2642 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.90 % Allowed : 19.01 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2411 helix: 1.27 (0.14), residues: 1405 sheet: -0.34 (0.35), residues: 202 loop : -1.12 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A2000 TYR 0.023 0.002 TYR A3369 PHE 0.024 0.002 PHE A3768 TRP 0.021 0.002 TRP A2084 HIS 0.008 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00442 (20062) covalent geometry : angle 0.71124 (27136) hydrogen bonds : bond 0.04128 ( 1102) hydrogen bonds : angle 4.68431 ( 3225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 0.656 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 1449 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: A 1704 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9046 (mt-10) REVERT: A 1762 TYR cc_start: 0.7850 (t80) cc_final: 0.7625 (t80) REVERT: A 1790 TYR cc_start: 0.8743 (m-80) cc_final: 0.7692 (t80) REVERT: A 1813 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8956 (mp) REVERT: A 2213 LEU cc_start: 0.8616 (tp) cc_final: 0.8167 (mp) REVERT: A 3013 ASN cc_start: 0.9518 (t0) cc_final: 0.9140 (t0) REVERT: A 3015 ARG cc_start: 0.9065 (ttp-170) cc_final: 0.8670 (ttp80) REVERT: A 3313 PHE cc_start: 0.8973 (t80) cc_final: 0.8470 (t80) REVERT: A 3330 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8628 (t80) REVERT: A 3394 MET cc_start: 0.9098 (tpp) cc_final: 0.8836 (tpp) REVERT: A 3538 ASN cc_start: 0.9094 (t0) cc_final: 0.8762 (p0) REVERT: A 3540 GLU cc_start: 0.9455 (mm-30) cc_final: 0.8773 (pm20) REVERT: A 3541 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8304 (mmm) REVERT: A 3616 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: A 3677 LEU cc_start: 0.9042 (mm) cc_final: 0.8558 (tt) REVERT: A 3702 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8599 (mpp) REVERT: A 3717 GLU cc_start: 0.9144 (tp30) cc_final: 0.8568 (pp20) REVERT: A 3722 MET cc_start: 0.8620 (mmm) cc_final: 0.8395 (mmm) REVERT: A 3768 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6336 (m-10) REVERT: A 3803 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8776 (pp) outliers start: 64 outliers final: 44 residues processed: 282 average time/residue: 0.1320 time to fit residues: 59.6412 Evaluate side-chains 284 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1544 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1794 PHE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2673 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3331 GLU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3616 GLU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3895 VAL Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 197 optimal weight: 0.1980 chunk 109 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 GLN A1554 HIS ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3442 ASN A3648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066743 restraints weight = 80774.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068703 restraints weight = 45655.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.069971 restraints weight = 31832.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.070883 restraints weight = 25346.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071440 restraints weight = 21793.892| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20062 Z= 0.140 Angle : 0.701 15.084 27136 Z= 0.347 Chirality : 0.043 0.315 3065 Planarity : 0.004 0.046 3416 Dihedral : 6.035 86.940 2642 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 2.50 % Allowed : 19.51 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2411 helix: 1.36 (0.14), residues: 1403 sheet: -0.25 (0.36), residues: 205 loop : -1.11 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2000 TYR 0.023 0.001 TYR A3369 PHE 0.022 0.001 PHE A3611 TRP 0.022 0.001 TRP A2084 HIS 0.007 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00318 (20062) covalent geometry : angle 0.70056 (27136) hydrogen bonds : bond 0.03922 ( 1102) hydrogen bonds : angle 4.56257 ( 3225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.725 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 1449 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: A 1704 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9062 (mt-10) REVERT: A 1762 TYR cc_start: 0.7828 (t80) cc_final: 0.7596 (t80) REVERT: A 1790 TYR cc_start: 0.8738 (m-80) cc_final: 0.7730 (t80) REVERT: A 1813 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 1919 PHE cc_start: 0.8052 (t80) cc_final: 0.7501 (t80) REVERT: A 1937 MET cc_start: 0.5014 (mmm) cc_final: 0.4058 (mtt) REVERT: A 2213 LEU cc_start: 0.8591 (tp) cc_final: 0.8160 (mp) REVERT: A 2225 LYS cc_start: 0.8737 (tttt) cc_final: 0.8474 (tptm) REVERT: A 2756 MET cc_start: 0.8795 (tpp) cc_final: 0.8143 (ttt) REVERT: A 2792 LEU cc_start: 0.9183 (mt) cc_final: 0.8695 (mp) REVERT: A 3013 ASN cc_start: 0.9486 (t0) cc_final: 0.9082 (t0) REVERT: A 3015 ARG cc_start: 0.9054 (ttp-170) cc_final: 0.8681 (ttp80) REVERT: A 3311 LYS cc_start: 0.9180 (tmmt) cc_final: 0.8899 (tmmt) REVERT: A 3313 PHE cc_start: 0.8992 (t80) cc_final: 0.8479 (t80) REVERT: A 3330 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8621 (t80) REVERT: A 3394 MET cc_start: 0.9090 (tpp) cc_final: 0.8877 (tpp) REVERT: A 3538 ASN cc_start: 0.9099 (t0) cc_final: 0.8448 (p0) REVERT: A 3540 GLU cc_start: 0.9463 (mm-30) cc_final: 0.8633 (pm20) REVERT: A 3541 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: A 3616 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: A 3677 LEU cc_start: 0.9025 (mm) cc_final: 0.8564 (tt) REVERT: A 3701 THR cc_start: 0.9435 (m) cc_final: 0.9133 (p) REVERT: A 3702 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8501 (mpp) REVERT: A 3717 GLU cc_start: 0.9127 (tp30) cc_final: 0.8570 (pp20) REVERT: A 3722 MET cc_start: 0.8580 (mmm) cc_final: 0.8354 (mmm) REVERT: A 3768 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6362 (m-10) outliers start: 55 outliers final: 42 residues processed: 279 average time/residue: 0.1404 time to fit residues: 62.5413 Evaluate side-chains 281 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1544 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1794 PHE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2207 ILE Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2673 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3331 GLU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3616 GLU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3895 VAL Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 141 optimal weight: 0.0670 chunk 231 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 GLN ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2931 ASN A3914 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067605 restraints weight = 81366.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069610 restraints weight = 46092.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071021 restraints weight = 31977.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071909 restraints weight = 25184.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072398 restraints weight = 21607.793| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20062 Z= 0.126 Angle : 0.695 15.192 27136 Z= 0.342 Chirality : 0.042 0.302 3065 Planarity : 0.004 0.046 3416 Dihedral : 5.899 88.023 2642 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 2.09 % Allowed : 19.78 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2411 helix: 1.44 (0.14), residues: 1401 sheet: -0.13 (0.37), residues: 204 loop : -1.11 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2000 TYR 0.023 0.001 TYR A3369 PHE 0.021 0.001 PHE A3768 TRP 0.022 0.001 TRP A2084 HIS 0.006 0.001 HIS A3517 Details of bonding type rmsd covalent geometry : bond 0.00286 (20062) covalent geometry : angle 0.69462 (27136) hydrogen bonds : bond 0.03737 ( 1102) hydrogen bonds : angle 4.49279 ( 3225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.858 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 1411 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 1449 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: A 1762 TYR cc_start: 0.7813 (t80) cc_final: 0.7575 (t80) REVERT: A 1790 TYR cc_start: 0.8724 (m-80) cc_final: 0.7790 (t80) REVERT: A 1919 PHE cc_start: 0.8021 (t80) cc_final: 0.7536 (t80) REVERT: A 1937 MET cc_start: 0.4888 (mmm) cc_final: 0.3922 (mtt) REVERT: A 2118 MET cc_start: 0.8592 (pmm) cc_final: 0.7679 (tpp) REVERT: A 2213 LEU cc_start: 0.8614 (tp) cc_final: 0.8206 (mp) REVERT: A 2496 LYS cc_start: 0.9236 (tptp) cc_final: 0.8660 (pttm) REVERT: A 2508 GLN cc_start: 0.9084 (tt0) cc_final: 0.8608 (tm-30) REVERT: A 2792 LEU cc_start: 0.9134 (mt) cc_final: 0.8615 (mp) REVERT: A 2793 SER cc_start: 0.9343 (m) cc_final: 0.9004 (p) REVERT: A 3013 ASN cc_start: 0.9473 (t0) cc_final: 0.9108 (t0) REVERT: A 3015 ARG cc_start: 0.9046 (ttp-170) cc_final: 0.8684 (ttp80) REVERT: A 3313 PHE cc_start: 0.8988 (t80) cc_final: 0.8469 (t80) REVERT: A 3330 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8597 (t80) REVERT: A 3394 MET cc_start: 0.9100 (tpp) cc_final: 0.8829 (tpp) REVERT: A 3398 MET cc_start: 0.8738 (mmt) cc_final: 0.8500 (mmm) REVERT: A 3538 ASN cc_start: 0.9102 (t0) cc_final: 0.8463 (p0) REVERT: A 3540 GLU cc_start: 0.9453 (mm-30) cc_final: 0.8635 (pm20) REVERT: A 3541 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: A 3701 THR cc_start: 0.9403 (m) cc_final: 0.9071 (p) REVERT: A 3702 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8491 (mpp) REVERT: A 3717 GLU cc_start: 0.9125 (tp30) cc_final: 0.8583 (pp20) REVERT: A 3722 MET cc_start: 0.8591 (mmm) cc_final: 0.8362 (mmm) REVERT: A 3875 MET cc_start: 0.8161 (mpp) cc_final: 0.7615 (mpp) outliers start: 46 outliers final: 38 residues processed: 288 average time/residue: 0.1357 time to fit residues: 62.4477 Evaluate side-chains 282 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1544 ASP Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1794 PHE Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2341 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2834 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3331 GLU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3895 VAL Chi-restraints excluded: chain A residue 4024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 163 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.089086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067418 restraints weight = 81524.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069323 restraints weight = 46834.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070603 restraints weight = 32724.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071369 restraints weight = 25834.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072075 restraints weight = 22520.542| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20062 Z= 0.136 Angle : 0.701 15.683 27136 Z= 0.345 Chirality : 0.042 0.295 3065 Planarity : 0.004 0.046 3416 Dihedral : 5.881 87.493 2642 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 2.13 % Allowed : 19.92 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2411 helix: 1.43 (0.14), residues: 1397 sheet: -0.04 (0.37), residues: 204 loop : -1.06 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2000 TYR 0.022 0.001 TYR A3369 PHE 0.032 0.001 PHE A2190 TRP 0.021 0.001 TRP A2084 HIS 0.007 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00308 (20062) covalent geometry : angle 0.70087 (27136) hydrogen bonds : bond 0.03741 ( 1102) hydrogen bonds : angle 4.49292 ( 3225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5415.43 seconds wall clock time: 93 minutes 35.05 seconds (5615.05 seconds total)