Starting phenix.real_space_refine on Fri Feb 6 01:40:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mfv_48239/02_2026/9mfv_48239.map" } resolution = 3.3 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 97 5.16 5 C 13461 2.51 5 N 3491 2.21 5 O 3953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21010 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2583, 20924 Classifications: {'peptide': 2583} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 2513} Chain breaks: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.13, per 1000 atoms: 0.20 Number of scatterers: 21010 At special positions: 0 Unit cell: (122.388, 160.146, 169.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 7 15.00 Mg 1 11.99 O 3953 8.00 N 3491 7.00 C 13461 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4930 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 17 sheets defined 64.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 1241 through 1250 Processing helix chain 'A' and resid 1257 through 1274 removed outlier: 3.814A pdb=" N SER A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A1274 " --> pdb=" O ARG A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 3.520A pdb=" N PHE A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 4.046A pdb=" N LYS A1286 " --> pdb=" O PHE A1282 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A1298 " --> pdb=" O MET A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1328 through 1334 removed outlier: 3.979A pdb=" N LYS A1334 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1345 removed outlier: 3.810A pdb=" N VAL A1342 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1379 removed outlier: 3.655A pdb=" N ARG A1360 " --> pdb=" O LYS A1356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1415 removed outlier: 4.093A pdb=" N ALA A1404 " --> pdb=" O VAL A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1422 removed outlier: 5.560A pdb=" N ASN A1419 " --> pdb=" O LYS A1416 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR A1420 " --> pdb=" O ALA A1417 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A1422 " --> pdb=" O ASN A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1459 removed outlier: 3.990A pdb=" N ASP A1430 " --> pdb=" O GLN A1426 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A1458 " --> pdb=" O ASP A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1469 Processing helix chain 'A' and resid 1469 through 1492 removed outlier: 3.530A pdb=" N SER A1478 " --> pdb=" O SER A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1502 Processing helix chain 'A' and resid 1505 through 1532 Processing helix chain 'A' and resid 1534 through 1540 Processing helix chain 'A' and resid 1542 through 1551 Processing helix chain 'A' and resid 1557 through 1567 removed outlier: 4.274A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.518A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A1613 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.660A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1667 removed outlier: 3.567A pdb=" N LYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1689 removed outlier: 4.621A pdb=" N TYR A1672 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1718 removed outlier: 3.878A pdb=" N LYS A1697 " --> pdb=" O ASN A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.635A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1745 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.641A pdb=" N ILE A1777 " --> pdb=" O PRO A1773 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.573A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 removed outlier: 4.298A pdb=" N LYS A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1937 removed outlier: 3.748A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1981 Processing helix chain 'A' and resid 1982 through 1985 removed outlier: 3.534A pdb=" N SER A1985 " --> pdb=" O PRO A1982 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1982 through 1985' Processing helix chain 'A' and resid 1990 through 2006 removed outlier: 3.963A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) removed outlier: 4.076A 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: 4.356A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A2013 " --> pdb=" O THR A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2044 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 4.024A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2221 through 2238 removed outlier: 5.165A pdb=" N ASP A2227 " --> pdb=" O SER A2223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A2236 " --> pdb=" O LYS A2232 " (cutoff:3.500A) Processing helix chain 'A' and resid 2239 through 2241 No H-bonds generated for 'chain 'A' and resid 2239 through 2241' Processing helix chain 'A' and resid 2242 through 2257 removed outlier: 3.513A pdb=" N LEU A2246 " --> pdb=" O SER A2242 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.355A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2297 removed outlier: 5.101A pdb=" N GLU A2285 " --> pdb=" O PHE A2281 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A2286 " --> pdb=" O ASN A2282 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2332 through 2346 removed outlier: 3.648A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2385 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 Processing helix chain 'A' and resid 2450 through 2459 removed outlier: 4.079A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A2455 " --> pdb=" O THR A2451 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2565 through 2579 removed outlier: 3.912A pdb=" N GLN A2569 " --> pdb=" O LYS A2565 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A2574 " --> pdb=" O ILE A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2581 No H-bonds generated for 'chain 'A' and resid 2580 through 2581' Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.372A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.530A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A2607 " --> pdb=" O CYS A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.862A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A2635 " --> pdb=" O THR A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.772A pdb=" N THR A2722 " --> pdb=" O GLU A2718 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.725A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2809 removed outlier: 3.543A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A2809 " --> pdb=" O ASP A2805 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.853A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.524A pdb=" N LEU A2863 " --> pdb=" O LYS A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2885 Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2911 Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.520A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3027 Processing helix chain 'A' and resid 3299 through 3307 removed outlier: 3.575A pdb=" N ARG A3305 " --> pdb=" O PHE A3301 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3319 removed outlier: 3.597A pdb=" N GLN A3312 " --> pdb=" O ASN A3308 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A3318 " --> pdb=" O SER A3314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A3319 " --> pdb=" O LYS A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 3.648A pdb=" N LEU A3337 " --> pdb=" O PHE A3334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3334 through 3337' Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.745A pdb=" N ALA A3343 " --> pdb=" O GLU A3339 " (cutoff:3.500A) Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3400 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 3.939A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A3417 " --> pdb=" O HIS A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3424 through 3426 No H-bonds generated for 'chain 'A' and resid 3424 through 3426' Processing helix chain 'A' and resid 3435 through 3447 removed outlier: 3.588A pdb=" N GLU A3441 " --> pdb=" O VAL A3437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A3445 " --> pdb=" O GLU A3441 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 3506 through 3513 removed outlier: 3.663A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3522 through 3538 removed outlier: 3.948A pdb=" N GLU A3526 " --> pdb=" O LYS A3522 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A3527 " --> pdb=" O GLU A3523 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A3530 " --> pdb=" O GLU A3526 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A3535 " --> pdb=" O ASP A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3573 removed outlier: 3.538A pdb=" N GLU A3546 " --> pdb=" O GLN A3542 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A3549 " --> pdb=" O ARG A3545 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A3560 " --> pdb=" O LYS A3556 " (cutoff:3.500A) Processing helix chain 'A' and resid 3579 through 3639 removed outlier: 3.835A pdb=" N LEU A3583 " --> pdb=" O GLU A3579 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A3591 " --> pdb=" O LEU A3587 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A3592 " --> pdb=" O ASN A3588 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A3593 " --> pdb=" O ASN A3589 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Proline residue: A3609 - end of helix removed outlier: 3.932A pdb=" N GLU A3616 " --> pdb=" O ASP A3612 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A3617 " --> pdb=" O ASN A3613 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A3624 " --> pdb=" O ILE A3620 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.767A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3687 Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 3.993A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.790A pdb=" N ALA A3718 " --> pdb=" O GLN A3714 " (cutoff:3.500A) Processing helix chain 'A' and resid 3741 through 3753 Processing helix chain 'A' and resid 3755 through 3766 removed outlier: 4.199A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3781 Processing helix chain 'A' and resid 3796 through 3806 Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 4.270A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3846 No H-bonds generated for 'chain 'A' and resid 3844 through 3846' Processing helix chain 'A' and resid 3847 through 3854 Processing helix chain 'A' and resid 3854 through 3862 Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3902 through 3915 removed outlier: 3.991A pdb=" N PHE A3915 " --> pdb=" O TRP A3911 " (cutoff:3.500A) Processing helix chain 'A' and resid 3916 through 3918 No H-bonds generated for 'chain 'A' and resid 3916 through 3918' Processing helix chain 'A' and resid 3922 through 3945 removed outlier: 3.914A pdb=" N LEU A3945 " --> pdb=" O ALA A3941 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.971A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3990 removed outlier: 3.808A pdb=" N ASP A3987 " --> pdb=" O ALA A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4016 Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.856A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.541A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1384 through 1387 removed outlier: 4.160A pdb=" N GLU A1384 " --> pdb=" O ARG A1396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1569 through 1574 Processing sheet with id=AA3, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.828A pdb=" N ILE A1596 " --> pdb=" O ILE A1579 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA5, first strand: chain 'A' and resid 1818 through 1821 removed outlier: 6.342A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A1917 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A1793 " --> pdb=" O ARG A1917 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1879 through 1881 Processing sheet with id=AA7, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.596A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA9, first strand: chain 'A' and resid 2358 through 2359 Processing sheet with id=AB1, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.161A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2473 through 2475 removed outlier: 3.798A pdb=" N GLU A2527 " --> pdb=" O LEU A2474 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.976A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.582A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3427 through 3429 removed outlier: 6.210A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER A3498 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A3407 " --> pdb=" O SER A3498 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id=AB7, first strand: chain 'A' and resid 3812 through 3813 removed outlier: 6.556A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR A3787 " --> pdb=" O PHE A3895 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4020 through 4021 1172 hydrogen bonds defined for protein. 3444 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: 5.03 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6741 1.34 - 1.46: 4063 1.46 - 1.58: 10468 1.58 - 1.69: 8 1.69 - 1.81: 156 Bond restraints: 21436 Sorted by residual: bond pdb=" N VAL A3656 " pdb=" CA VAL A3656 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.19e+00 bond pdb=" N ILE A3658 " pdb=" CA ILE A3658 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.03e+00 bond pdb=" N LYS A3952 " pdb=" CA LYS A3952 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N PHE A3950 " pdb=" CA PHE A3950 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.63e+00 ... (remaining 21431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 28469 1.86 - 3.72: 423 3.72 - 5.58: 73 5.58 - 7.44: 18 7.44 - 9.30: 3 Bond angle restraints: 28986 Sorted by residual: angle pdb=" N ILE A3462 " pdb=" CA ILE A3462 " pdb=" C ILE A3462 " ideal model delta sigma weight residual 112.98 107.83 5.15 1.25e+00 6.40e-01 1.70e+01 angle pdb=" N SER A3810 " pdb=" CA SER A3810 " pdb=" C SER A3810 " ideal model delta sigma weight residual 110.80 118.76 -7.96 2.13e+00 2.20e-01 1.40e+01 angle pdb=" N GLN A1362 " pdb=" CA GLN A1362 " pdb=" CB GLN A1362 " ideal model delta sigma weight residual 110.12 115.45 -5.33 1.47e+00 4.63e-01 1.31e+01 angle pdb=" N ASN A3025 " pdb=" CA ASN A3025 " pdb=" C ASN A3025 " ideal model delta sigma weight residual 111.36 107.54 3.82 1.09e+00 8.42e-01 1.23e+01 angle pdb=" CA LYS A3660 " pdb=" C LYS A3660 " pdb=" O LYS A3660 " ideal model delta sigma weight residual 122.64 118.27 4.37 1.25e+00 6.40e-01 1.22e+01 ... (remaining 28981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 11997 21.89 - 43.78: 796 43.78 - 65.67: 113 65.67 - 87.57: 31 87.57 - 109.46: 9 Dihedral angle restraints: 12946 sinusoidal: 5355 harmonic: 7591 Sorted by residual: dihedral pdb=" CA GLU A3809 " pdb=" C GLU A3809 " pdb=" N SER A3810 " pdb=" CA SER A3810 " ideal model delta harmonic sigma weight residual 180.00 139.07 40.93 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA LEU A2471 " pdb=" C LEU A2471 " pdb=" N THR A2472 " pdb=" CA THR A2472 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" O2A ADP A4102 " pdb=" O3A ADP A4102 " pdb=" PA ADP A4102 " pdb=" PB ADP A4102 " ideal model delta sinusoidal sigma weight residual -60.00 49.46 -109.46 1 2.00e+01 2.50e-03 3.20e+01 ... (remaining 12943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2306 0.039 - 0.078: 745 0.078 - 0.117: 187 0.117 - 0.155: 37 0.155 - 0.194: 9 Chirality restraints: 3284 Sorted by residual: chirality pdb=" CA THR A2518 " pdb=" N THR A2518 " pdb=" C THR A2518 " pdb=" CB THR A2518 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA ILE A3658 " pdb=" N ILE A3658 " pdb=" C ILE A3658 " pdb=" CB ILE A3658 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CA VAL A3656 " pdb=" N VAL A3656 " pdb=" C VAL A3656 " pdb=" CB VAL A3656 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 3281 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A3655 " 0.360 9.50e-02 1.11e+02 1.61e-01 1.60e+01 pdb=" NE ARG A3655 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A3655 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A3655 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A3655 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2518 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO A2519 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A2519 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2519 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A3404 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A3405 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A3405 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A3405 " -0.027 5.00e-02 4.00e+02 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 112 2.50 - 3.10: 15913 3.10 - 3.70: 32454 3.70 - 4.30: 46617 4.30 - 4.90: 78055 Nonbonded interactions: 173151 Sorted by model distance: nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4104 " model vdw 1.903 2.170 nonbonded pdb=" O1G ATP A4101 " pdb="MG MG A4104 " model vdw 1.943 2.170 nonbonded pdb=" OE2 GLU A2195 " pdb="MG MG A4104 " model vdw 1.995 2.170 nonbonded pdb=" O ASP A2127 " pdb=" OG1 THR A2131 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR A3330 " pdb=" OE1 GLU A3392 " model vdw 2.159 3.040 ... (remaining 173146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.580 Find NCS groups from input model: 0.090 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.004 0.037 21436 Z= 0.191 Angle : 0.595 9.297 28986 Z= 0.322 Chirality : 0.042 0.194 3284 Planarity : 0.004 0.161 3651 Dihedral : 14.899 109.458 8016 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.08 % Allowed : 0.51 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 2579 helix: 1.28 (0.14), residues: 1499 sheet: -1.27 (0.37), residues: 199 loop : -1.11 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1978 TYR 0.016 0.001 TYR A2571 PHE 0.018 0.001 PHE A2877 TRP 0.022 0.001 TRP A2084 HIS 0.004 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00402 (21436) covalent geometry : angle 0.59463 (28986) hydrogen bonds : bond 0.13412 ( 1168) hydrogen bonds : angle 5.65134 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 533 time to evaluate : 0.760 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 3608 PHE cc_start: 0.7974 (m-80) cc_final: 0.7712 (m-80) REVERT: A 3895 PHE cc_start: 0.6925 (p90) cc_final: 0.6370 (p90) outliers start: 2 outliers final: 0 residues processed: 535 average time/residue: 0.1752 time to fit residues: 137.9310 Evaluate side-chains 213 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1530 GLN A1732 GLN ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 ASN A2634 ASN A3312 GLN A3596 ASN A3821 ASN A3843 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.085438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066169 restraints weight = 68069.836| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.97 r_work: 0.3119 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21436 Z= 0.151 Angle : 0.636 9.069 28986 Z= 0.327 Chirality : 0.041 0.186 3284 Planarity : 0.004 0.039 3651 Dihedral : 6.075 107.803 2827 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.40 % Allowed : 9.88 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2579 helix: 1.47 (0.13), residues: 1515 sheet: -1.14 (0.36), residues: 213 loop : -1.02 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A4028 TYR 0.017 0.001 TYR A2345 PHE 0.019 0.001 PHE A1669 TRP 0.018 0.001 TRP A2084 HIS 0.007 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00345 (21436) covalent geometry : angle 0.63563 (28986) hydrogen bonds : bond 0.04205 ( 1168) hydrogen bonds : angle 4.40041 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.817 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 1485 MET cc_start: 0.9147 (ttp) cc_final: 0.8724 (ppp) REVERT: A 1561 PHE cc_start: 0.8871 (m-10) cc_final: 0.8617 (m-10) REVERT: A 1657 THR cc_start: 0.9155 (m) cc_final: 0.8916 (p) REVERT: A 1699 GLU cc_start: 0.9126 (pt0) cc_final: 0.8839 (pt0) REVERT: A 1823 ASP cc_start: 0.7340 (t0) cc_final: 0.7005 (t0) REVERT: A 2951 GLU cc_start: 0.8255 (mp0) cc_final: 0.7740 (pm20) REVERT: A 3788 MET cc_start: 0.8744 (ttt) cc_final: 0.8289 (ttp) REVERT: A 3843 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 3883 LYS cc_start: 0.8600 (tttt) cc_final: 0.8222 (tmtt) REVERT: A 3895 PHE cc_start: 0.7285 (p90) cc_final: 0.6879 (p90) REVERT: A 3972 LEU cc_start: 0.9183 (mt) cc_final: 0.8931 (mt) REVERT: A 4023 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7657 (mt) outliers start: 33 outliers final: 16 residues processed: 250 average time/residue: 0.1524 time to fit residues: 59.2245 Evaluate side-chains 187 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 2313 VAL Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3843 ASN Chi-restraints excluded: chain A residue 3933 SER Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 94 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1326 GLN ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3308 ASN A3399 ASN A3714 GLN A3843 ASN A3845 GLN A3914 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063633 restraints weight = 69151.436| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.97 r_work: 0.3042 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21436 Z= 0.175 Angle : 0.592 7.806 28986 Z= 0.304 Chirality : 0.042 0.246 3284 Planarity : 0.004 0.042 3651 Dihedral : 6.111 112.648 2827 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.04 % Allowed : 12.17 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.77 (0.17), residues: 2579 helix: 1.53 (0.13), residues: 1535 sheet: -0.88 (0.36), residues: 208 loop : -1.00 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2433 TYR 0.013 0.001 TYR A1790 PHE 0.017 0.002 PHE A2972 TRP 0.018 0.001 TRP A2084 HIS 0.007 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00402 (21436) covalent geometry : angle 0.59238 (28986) hydrogen bonds : bond 0.03944 ( 1168) hydrogen bonds : angle 4.21986 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 GLU cc_start: 0.9275 (tt0) cc_final: 0.8579 (tm-30) REVERT: A 1561 PHE cc_start: 0.8873 (m-10) cc_final: 0.8652 (m-10) REVERT: A 1699 GLU cc_start: 0.9109 (pt0) cc_final: 0.8812 (pt0) REVERT: A 1762 TYR cc_start: 0.8694 (t80) cc_final: 0.8348 (t80) REVERT: A 1790 TYR cc_start: 0.9004 (m-80) cc_final: 0.8621 (m-80) REVERT: A 1918 GLU cc_start: 0.9241 (mt-10) cc_final: 0.9004 (mt-10) REVERT: A 1945 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9156 (tt) REVERT: A 1963 MET cc_start: 0.9262 (mmt) cc_final: 0.9047 (mmm) REVERT: A 2401 GLU cc_start: 0.8596 (pp20) cc_final: 0.8369 (pp20) REVERT: A 2917 MET cc_start: 0.9493 (mmm) cc_final: 0.9147 (mmm) REVERT: A 3475 ASN cc_start: 0.7617 (m-40) cc_final: 0.7229 (p0) REVERT: A 3623 LYS cc_start: 0.9258 (mmtm) cc_final: 0.9044 (mmtt) REVERT: A 3788 MET cc_start: 0.8827 (ttt) cc_final: 0.8494 (ttp) REVERT: A 3843 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8532 (t0) REVERT: A 3883 LYS cc_start: 0.8520 (tttt) cc_final: 0.8128 (tmtt) REVERT: A 4023 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8066 (mt) outliers start: 48 outliers final: 26 residues processed: 220 average time/residue: 0.1376 time to fit residues: 48.5129 Evaluate side-chains 183 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1680 ILE Chi-restraints excluded: chain A residue 1692 ASP Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1945 LEU Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 2180 ASN Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2833 THR Chi-restraints excluded: chain A residue 2881 ILE Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3843 ASN Chi-restraints excluded: chain A residue 3933 SER Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 4010 LEU Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1891 HIS A3471 ASN A3580 ASN A3842 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062163 restraints weight = 69322.925| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.95 r_work: 0.3016 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21436 Z= 0.191 Angle : 0.586 7.333 28986 Z= 0.301 Chirality : 0.041 0.175 3284 Planarity : 0.004 0.044 3651 Dihedral : 6.144 114.968 2827 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.59 % Allowed : 13.32 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.89 (0.17), residues: 2579 helix: 1.63 (0.13), residues: 1529 sheet: -1.00 (0.36), residues: 206 loop : -0.91 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2126 TYR 0.010 0.001 TYR A2630 PHE 0.020 0.002 PHE A1826 TRP 0.020 0.001 TRP A2301 HIS 0.007 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00434 (21436) covalent geometry : angle 0.58576 (28986) hydrogen bonds : bond 0.03888 ( 1168) hydrogen bonds : angle 4.17279 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1284 MET cc_start: -0.0273 (OUTLIER) cc_final: -0.0514 (mtt) REVERT: A 1368 GLU cc_start: 0.9288 (tt0) cc_final: 0.8567 (tm-30) REVERT: A 1699 GLU cc_start: 0.9125 (pt0) cc_final: 0.8841 (pt0) REVERT: A 1790 TYR cc_start: 0.9130 (m-80) cc_final: 0.8762 (m-80) REVERT: A 1918 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9078 (mt-10) REVERT: A 2330 SER cc_start: 0.8990 (m) cc_final: 0.8597 (p) REVERT: A 2401 GLU cc_start: 0.8569 (pp20) cc_final: 0.8350 (pp20) REVERT: A 2670 GLU cc_start: 0.8924 (tt0) cc_final: 0.8378 (tm-30) REVERT: A 2768 ILE cc_start: 0.9161 (tt) cc_final: 0.8939 (tp) REVERT: A 2856 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9334 (tp) REVERT: A 2917 MET cc_start: 0.9470 (mmm) cc_final: 0.9207 (mmm) REVERT: A 2951 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: A 3475 ASN cc_start: 0.8203 (m-40) cc_final: 0.7863 (p0) REVERT: A 3605 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7544 (mt-10) REVERT: A 3843 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 3873 MET cc_start: 0.7837 (tmm) cc_final: 0.7197 (tmm) REVERT: A 3895 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7135 (p90) outliers start: 61 outliers final: 36 residues processed: 212 average time/residue: 0.1331 time to fit residues: 45.8435 Evaluate side-chains 191 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1351 GLU Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2180 ASN Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2833 THR Chi-restraints excluded: chain A residue 2856 LEU Chi-restraints excluded: chain A residue 2950 LYS Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3301 PHE Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3451 ILE Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 GLU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3843 ASN Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 3946 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 25 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3843 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.063265 restraints weight = 68677.896| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.90 r_work: 0.3044 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21436 Z= 0.137 Angle : 0.550 9.088 28986 Z= 0.280 Chirality : 0.041 0.307 3284 Planarity : 0.003 0.043 3651 Dihedral : 5.984 113.635 2827 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.21 % Allowed : 14.12 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2579 helix: 1.76 (0.13), residues: 1532 sheet: -0.89 (0.36), residues: 205 loop : -0.82 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2126 TYR 0.011 0.001 TYR A2571 PHE 0.014 0.001 PHE A2827 TRP 0.016 0.001 TRP A2084 HIS 0.007 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00310 (21436) covalent geometry : angle 0.54994 (28986) hydrogen bonds : bond 0.03577 ( 1168) hydrogen bonds : angle 4.03105 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 GLU cc_start: 0.9246 (tt0) cc_final: 0.8576 (tm-30) REVERT: A 1485 MET cc_start: 0.9183 (ttp) cc_final: 0.8717 (ppp) REVERT: A 1589 VAL cc_start: 0.9356 (t) cc_final: 0.9151 (t) REVERT: A 1683 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9111 (tp) REVERT: A 1699 GLU cc_start: 0.9060 (pt0) cc_final: 0.8776 (pt0) REVERT: A 1790 TYR cc_start: 0.9055 (m-80) cc_final: 0.8649 (m-80) REVERT: A 1918 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9035 (mt-10) REVERT: A 2330 SER cc_start: 0.8909 (m) cc_final: 0.8384 (p) REVERT: A 2401 GLU cc_start: 0.8600 (pp20) cc_final: 0.8360 (pp20) REVERT: A 2428 MET cc_start: 0.8615 (ttp) cc_final: 0.8271 (ttp) REVERT: A 2572 GLU cc_start: 0.9083 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 2670 GLU cc_start: 0.8948 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 2856 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9324 (tp) REVERT: A 2917 MET cc_start: 0.9463 (mmm) cc_final: 0.9225 (mmm) REVERT: A 2951 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: A 3475 ASN cc_start: 0.8155 (m-40) cc_final: 0.7892 (p0) REVERT: A 3605 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7539 (mt-10) REVERT: A 3623 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8967 (mmtt) REVERT: A 3722 MET cc_start: 0.8483 (mmt) cc_final: 0.8260 (mmt) REVERT: A 3788 MET cc_start: 0.8794 (ttt) cc_final: 0.8371 (ttp) REVERT: A 3843 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8800 (t0) REVERT: A 3873 MET cc_start: 0.7828 (tmm) cc_final: 0.7181 (tmm) outliers start: 52 outliers final: 31 residues processed: 219 average time/residue: 0.1311 time to fit residues: 45.9991 Evaluate side-chains 187 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2856 LEU Chi-restraints excluded: chain A residue 2950 LYS Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 GLU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3843 ASN Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 105 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4013 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.081791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063022 restraints weight = 69046.903| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.96 r_work: 0.3054 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21436 Z= 0.141 Angle : 0.557 7.859 28986 Z= 0.282 Chirality : 0.040 0.218 3284 Planarity : 0.003 0.042 3651 Dihedral : 5.943 112.869 2827 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.29 % Allowed : 15.31 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2579 helix: 1.85 (0.13), residues: 1526 sheet: -0.73 (0.37), residues: 203 loop : -0.76 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3015 TYR 0.010 0.001 TYR A2571 PHE 0.022 0.001 PHE A3961 TRP 0.016 0.001 TRP A2084 HIS 0.008 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00322 (21436) covalent geometry : angle 0.55660 (28986) hydrogen bonds : bond 0.03538 ( 1168) hydrogen bonds : angle 3.99569 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 GLU cc_start: 0.9263 (tt0) cc_final: 0.8570 (tm-30) REVERT: A 1485 MET cc_start: 0.9218 (ttp) cc_final: 0.8719 (ppp) REVERT: A 1632 ASP cc_start: 0.9209 (t0) cc_final: 0.8800 (p0) REVERT: A 1699 GLU cc_start: 0.9081 (pt0) cc_final: 0.8788 (pt0) REVERT: A 1790 TYR cc_start: 0.9099 (m-80) cc_final: 0.8682 (m-80) REVERT: A 1852 ARG cc_start: 0.8704 (mtm180) cc_final: 0.7999 (mtm-85) REVERT: A 2330 SER cc_start: 0.8971 (m) cc_final: 0.8434 (p) REVERT: A 2572 GLU cc_start: 0.9095 (tt0) cc_final: 0.8791 (tm-30) REVERT: A 2670 GLU cc_start: 0.8970 (tt0) cc_final: 0.8377 (tm-30) REVERT: A 2856 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9361 (tp) REVERT: A 2917 MET cc_start: 0.9445 (mmm) cc_final: 0.9180 (mmm) REVERT: A 2951 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 3475 ASN cc_start: 0.8251 (m-40) cc_final: 0.7986 (p0) REVERT: A 3605 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7552 (mt-10) REVERT: A 3623 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8957 (mmtt) REVERT: A 3722 MET cc_start: 0.8512 (mmt) cc_final: 0.8272 (mmt) REVERT: A 3788 MET cc_start: 0.8820 (ttt) cc_final: 0.8431 (ttp) REVERT: A 3843 ASN cc_start: 0.9213 (t0) cc_final: 0.8524 (t0) REVERT: A 3873 MET cc_start: 0.7775 (tmm) cc_final: 0.7082 (tmm) outliers start: 54 outliers final: 35 residues processed: 208 average time/residue: 0.1462 time to fit residues: 49.0275 Evaluate side-chains 186 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1644 ILE Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2856 LEU Chi-restraints excluded: chain A residue 2950 LYS Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 GLU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3801 ILE Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 179 optimal weight: 0.0170 chunk 125 optimal weight: 5.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.081205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063472 restraints weight = 67803.551| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.73 r_work: 0.3081 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21436 Z= 0.140 Angle : 0.559 13.367 28986 Z= 0.281 Chirality : 0.040 0.322 3284 Planarity : 0.003 0.042 3651 Dihedral : 5.903 111.735 2827 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.33 % Allowed : 15.65 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2579 helix: 1.92 (0.13), residues: 1522 sheet: -0.68 (0.37), residues: 203 loop : -0.67 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3015 TYR 0.010 0.001 TYR A2571 PHE 0.016 0.001 PHE A3961 TRP 0.016 0.001 TRP A2084 HIS 0.008 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00318 (21436) covalent geometry : angle 0.55900 (28986) hydrogen bonds : bond 0.03501 ( 1168) hydrogen bonds : angle 3.96342 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1485 MET cc_start: 0.9226 (ttp) cc_final: 0.8708 (ppp) REVERT: A 1543 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (p0) REVERT: A 1632 ASP cc_start: 0.9197 (t0) cc_final: 0.8774 (p0) REVERT: A 1683 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9133 (tp) REVERT: A 1767 GLU cc_start: 0.8105 (tp30) cc_final: 0.7827 (tm-30) REVERT: A 1790 TYR cc_start: 0.9065 (m-80) cc_final: 0.8628 (m-80) REVERT: A 1852 ARG cc_start: 0.8703 (mtm180) cc_final: 0.7981 (mtm-85) REVERT: A 1918 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8953 (mt-10) REVERT: A 2330 SER cc_start: 0.8945 (m) cc_final: 0.8435 (p) REVERT: A 2572 GLU cc_start: 0.9032 (tt0) cc_final: 0.8737 (tm-30) REVERT: A 2670 GLU cc_start: 0.8922 (tt0) cc_final: 0.8323 (tm-30) REVERT: A 2917 MET cc_start: 0.9411 (mmm) cc_final: 0.9135 (mmm) REVERT: A 2951 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: A 3475 ASN cc_start: 0.8274 (m-40) cc_final: 0.7997 (p0) REVERT: A 3541 MET cc_start: 0.8237 (tpt) cc_final: 0.7907 (tpp) REVERT: A 3605 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7558 (mt-10) REVERT: A 3623 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8973 (mmtt) REVERT: A 3700 MET cc_start: 0.8991 (ttm) cc_final: 0.8741 (ttm) REVERT: A 3788 MET cc_start: 0.8793 (ttt) cc_final: 0.8400 (ttp) REVERT: A 3873 MET cc_start: 0.7786 (tmm) cc_final: 0.7092 (tmm) outliers start: 55 outliers final: 44 residues processed: 208 average time/residue: 0.1437 time to fit residues: 48.3280 Evaluate side-chains 200 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1543 ASP Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1593 ASN Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1838 ILE Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 1958 SER Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2950 LYS Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3451 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3606 GLU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3682 VAL Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3801 ILE Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 230 optimal weight: 2.9990 chunk 255 optimal weight: 0.0020 chunk 181 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 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 = 0.3607 r_free = 0.3607 target = 0.083051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065335 restraints weight = 66792.804| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.79 r_work: 0.3090 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21436 Z= 0.106 Angle : 0.547 14.736 28986 Z= 0.272 Chirality : 0.040 0.360 3284 Planarity : 0.003 0.042 3651 Dihedral : 5.705 105.875 2827 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 16.28 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2579 helix: 1.98 (0.13), residues: 1519 sheet: -0.31 (0.39), residues: 189 loop : -0.65 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3015 TYR 0.013 0.001 TYR A3927 PHE 0.023 0.001 PHE A2485 TRP 0.014 0.001 TRP A2084 HIS 0.009 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00233 (21436) covalent geometry : angle 0.54720 (28986) hydrogen bonds : bond 0.03276 ( 1168) hydrogen bonds : angle 3.86057 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1384 GLU cc_start: 0.7964 (tp30) cc_final: 0.7665 (mt-10) REVERT: A 1485 MET cc_start: 0.9242 (ttp) cc_final: 0.8570 (ppp) REVERT: A 1543 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8529 (p0) REVERT: A 1632 ASP cc_start: 0.8979 (t0) cc_final: 0.8668 (p0) REVERT: A 1767 GLU cc_start: 0.8089 (tp30) cc_final: 0.7875 (tm-30) REVERT: A 1790 TYR cc_start: 0.8933 (m-80) cc_final: 0.8580 (m-80) REVERT: A 1838 ILE cc_start: 0.8916 (mm) cc_final: 0.8615 (tp) REVERT: A 1852 ARG cc_start: 0.8690 (mtm180) cc_final: 0.7950 (mtm-85) REVERT: A 1918 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8941 (mt-10) REVERT: A 2124 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 2330 SER cc_start: 0.8908 (m) cc_final: 0.8358 (p) REVERT: A 2520 GLU cc_start: 0.8866 (mp0) cc_final: 0.8592 (pm20) REVERT: A 2572 GLU cc_start: 0.9036 (tt0) cc_final: 0.8774 (tm-30) REVERT: A 2670 GLU cc_start: 0.8884 (tt0) cc_final: 0.8236 (tm-30) REVERT: A 2951 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: A 3311 LYS cc_start: 0.8666 (mptt) cc_final: 0.8393 (mptt) REVERT: A 3475 ASN cc_start: 0.8133 (m-40) cc_final: 0.7614 (p0) REVERT: A 3579 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6288 (tm-30) REVERT: A 3605 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7597 (mt-10) REVERT: A 3623 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8987 (mmtt) REVERT: A 3700 MET cc_start: 0.9007 (ttm) cc_final: 0.8717 (ttm) REVERT: A 3788 MET cc_start: 0.8751 (ttt) cc_final: 0.8373 (ttp) REVERT: A 3873 MET cc_start: 0.7727 (tmm) cc_final: 0.6998 (tmm) REVERT: A 3928 CYS cc_start: 0.9601 (m) cc_final: 0.9290 (m) outliers start: 46 outliers final: 36 residues processed: 213 average time/residue: 0.1472 time to fit residues: 50.2196 Evaluate side-chains 196 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1543 ASP Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1593 ASN Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2422 SER Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3024 LEU Chi-restraints excluded: chain A residue 3301 PHE Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3451 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3615 VAL Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3704 CYS Chi-restraints excluded: chain A residue 3726 LEU Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 134 optimal weight: 0.7980 chunk 180 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 chunk 195 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 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 = 0.3601 r_free = 0.3601 target = 0.083486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066037 restraints weight = 67159.032| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.75 r_work: 0.3144 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21436 Z= 0.101 Angle : 0.557 13.231 28986 Z= 0.274 Chirality : 0.039 0.310 3284 Planarity : 0.003 0.041 3651 Dihedral : 5.545 97.504 2827 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.48 % Allowed : 17.22 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.17), residues: 2579 helix: 1.99 (0.13), residues: 1524 sheet: -0.17 (0.41), residues: 182 loop : -0.63 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3015 TYR 0.010 0.001 TYR A2571 PHE 0.026 0.001 PHE A1826 TRP 0.014 0.001 TRP A2084 HIS 0.009 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00220 (21436) covalent geometry : angle 0.55745 (28986) hydrogen bonds : bond 0.03179 ( 1168) hydrogen bonds : angle 3.78283 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1384 GLU cc_start: 0.8065 (tp30) cc_final: 0.7662 (mt-10) REVERT: A 1485 MET cc_start: 0.9238 (ttp) cc_final: 0.8556 (ppp) REVERT: A 1543 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (p0) REVERT: A 1632 ASP cc_start: 0.8945 (t0) cc_final: 0.8614 (p0) REVERT: A 1790 TYR cc_start: 0.8856 (m-80) cc_final: 0.8497 (m-80) REVERT: A 1838 ILE cc_start: 0.8881 (mm) cc_final: 0.8591 (tp) REVERT: A 1852 ARG cc_start: 0.8688 (mtm180) cc_final: 0.7946 (mtm-85) REVERT: A 1918 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8927 (mt-10) REVERT: A 2124 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: A 2330 SER cc_start: 0.8838 (m) cc_final: 0.8224 (p) REVERT: A 2520 GLU cc_start: 0.8850 (mp0) cc_final: 0.8509 (pm20) REVERT: A 2572 GLU cc_start: 0.8985 (tt0) cc_final: 0.8752 (tm-30) REVERT: A 2670 GLU cc_start: 0.8878 (tt0) cc_final: 0.8211 (tm-30) REVERT: A 2819 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8618 (tp30) REVERT: A 2917 MET cc_start: 0.9198 (mmm) cc_final: 0.8956 (mmm) REVERT: A 2951 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: A 3311 LYS cc_start: 0.8681 (mptt) cc_final: 0.8449 (mptt) REVERT: A 3475 ASN cc_start: 0.8084 (m-40) cc_final: 0.7610 (p0) REVERT: A 3605 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7753 (mt-10) REVERT: A 3623 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8922 (mmtt) REVERT: A 3700 MET cc_start: 0.8964 (ttm) cc_final: 0.8727 (ttm) REVERT: A 3788 MET cc_start: 0.8635 (ttt) cc_final: 0.8295 (ttp) REVERT: A 3873 MET cc_start: 0.7678 (tmm) cc_final: 0.6962 (tmm) outliers start: 35 outliers final: 26 residues processed: 208 average time/residue: 0.1472 time to fit residues: 49.3982 Evaluate side-chains 195 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1543 ASP Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1772 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3451 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3615 VAL Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 134 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 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 = 0.3612 r_free = 0.3612 target = 0.083555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065621 restraints weight = 68766.983| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.86 r_work: 0.3154 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21436 Z= 0.110 Angle : 0.565 13.955 28986 Z= 0.278 Chirality : 0.040 0.317 3284 Planarity : 0.003 0.040 3651 Dihedral : 5.469 91.172 2827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.53 % Allowed : 17.60 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.17), residues: 2579 helix: 1.99 (0.13), residues: 1526 sheet: -0.09 (0.40), residues: 183 loop : -0.58 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3015 TYR 0.009 0.001 TYR A2571 PHE 0.023 0.001 PHE A1826 TRP 0.014 0.001 TRP A2084 HIS 0.009 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00245 (21436) covalent geometry : angle 0.56496 (28986) hydrogen bonds : bond 0.03215 ( 1168) hydrogen bonds : angle 3.76699 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1384 GLU cc_start: 0.8069 (tp30) cc_final: 0.7691 (tp30) REVERT: A 1485 MET cc_start: 0.9224 (ttp) cc_final: 0.8511 (ppp) REVERT: A 1543 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8474 (p0) REVERT: A 1632 ASP cc_start: 0.8972 (t0) cc_final: 0.8528 (p0) REVERT: A 1678 MET cc_start: 0.8933 (tmm) cc_final: 0.8656 (tmm) REVERT: A 1790 TYR cc_start: 0.8879 (m-80) cc_final: 0.8553 (m-80) REVERT: A 1838 ILE cc_start: 0.8900 (mm) cc_final: 0.8615 (tp) REVERT: A 1852 ARG cc_start: 0.8686 (mtm180) cc_final: 0.7939 (mtm-85) REVERT: A 1918 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8941 (mt-10) REVERT: A 2124 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 2330 SER cc_start: 0.8794 (m) cc_final: 0.8189 (p) REVERT: A 2520 GLU cc_start: 0.8846 (mp0) cc_final: 0.8613 (pm20) REVERT: A 2670 GLU cc_start: 0.8847 (tt0) cc_final: 0.8240 (tm-30) REVERT: A 2917 MET cc_start: 0.9093 (mmm) cc_final: 0.8756 (mmm) REVERT: A 2951 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: A 3311 LYS cc_start: 0.8714 (mptt) cc_final: 0.8496 (mptt) REVERT: A 3475 ASN cc_start: 0.8121 (m-40) cc_final: 0.7674 (p0) REVERT: A 3605 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7750 (mt-10) REVERT: A 3623 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8956 (mmtt) REVERT: A 3722 MET cc_start: 0.8406 (mmt) cc_final: 0.8174 (mmt) REVERT: A 3788 MET cc_start: 0.8633 (ttt) cc_final: 0.8288 (ttp) REVERT: A 3808 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7414 (pptt) outliers start: 36 outliers final: 29 residues processed: 190 average time/residue: 0.1430 time to fit residues: 43.9168 Evaluate side-chains 188 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1543 ASP Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 1739 ASP Chi-restraints excluded: chain A residue 1772 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1928 THR Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2891 ILE Chi-restraints excluded: chain A residue 2951 GLU Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3451 ILE Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3615 VAL Chi-restraints excluded: chain A residue 3726 LEU Chi-restraints excluded: chain A residue 3808 LYS Chi-restraints excluded: chain A residue 3946 VAL Chi-restraints excluded: chain A residue 3993 VAL Chi-restraints excluded: chain A residue 4023 ILE Chi-restraints excluded: chain A residue 4081 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 219 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A3826 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.081018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063339 restraints weight = 68060.347| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.75 r_work: 0.3109 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21436 Z= 0.171 Angle : 0.602 13.860 28986 Z= 0.299 Chirality : 0.041 0.316 3284 Planarity : 0.003 0.039 3651 Dihedral : 5.699 86.871 2827 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.57 % Allowed : 17.56 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2579 helix: 1.98 (0.13), residues: 1525 sheet: -0.17 (0.40), residues: 183 loop : -0.56 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3015 TYR 0.014 0.001 TYR A3927 PHE 0.022 0.001 PHE A1826 TRP 0.015 0.001 TRP A2084 HIS 0.009 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00389 (21436) covalent geometry : angle 0.60238 (28986) hydrogen bonds : bond 0.03578 ( 1168) hydrogen bonds : angle 3.89418 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4639.18 seconds wall clock time: 80 minutes 45.33 seconds (4845.33 seconds total)