Starting phenix.real_space_refine on Fri Feb 6 01:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mfx_48241/02_2026/9mfx_48241.map" } resolution = 3.2 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= 0.035 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 98 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 14 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: 21011 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2583, 20925 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: 4.95, per 1000 atoms: 0.24 Number of scatterers: 21011 At special positions: 0 Unit cell: (122.674, 160.865, 168.966, 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 98 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: 1.82 Conformation dependent library (CDL) restraints added in 1.0 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: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 1241 through 1250 Processing helix chain 'A' and resid 1257 through 1274 removed outlier: 3.815A pdb=" N SER A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A1274 " --> pdb=" O ARG A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 3.521A 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: 3.809A pdb=" N VAL A1342 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1379 removed outlier: 3.654A pdb=" N ARG A1360 " --> pdb=" O LYS A1356 " (cutoff:3.500A) removed outlier: 3.511A 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: 4.264A pdb=" N LYS A1422 " --> pdb=" O ASN A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1459 removed outlier: 3.989A 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: 4.273A 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: 4.851A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1633 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: 4.166A 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: 4.622A 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: 3.877A pdb=" N LYS A1697 " --> pdb=" O ASN A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.636A 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: 3.533A 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: 5.164A pdb=" N ASP A2227 " --> pdb=" O SER A2223 " (cutoff:3.500A) removed outlier: 3.510A 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: 3.991A 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: 5.100A 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: 3.913A 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: 3.907A 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: 3.724A 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: 3.523A 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: 3.647A 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: 3.744A 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: 3.940A 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: 3.662A 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: 3.537A 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: 3.817A 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: 3.567A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3658 removed outlier: 3.867A 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: 3.791A 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: 4.137A 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: 3.990A 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: 3.675A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) removed outlier: 4.215A 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 4092 removed outlier: 3.542A 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: 6.977A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.670A 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: 6.788A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 3.764A 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: 6.284A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (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: 3.975A 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: 6.895A 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: 7.950A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.556A 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: 6.521A 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: 7.379A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 5.882A 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: 7.230A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.857A 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: 6.701A 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: 5.893A 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 1169 hydrogen bonds defined for protein. 3438 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: 6.03 Time building geometry restraints manager: 2.47 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: 6742 1.34 - 1.46: 4134 1.46 - 1.58: 10395 1.58 - 1.69: 8 1.69 - 1.81: 158 Bond restraints: 21437 Sorted by residual: bond pdb=" N VAL A1639 " pdb=" CA VAL A1639 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 8.99e+00 bond pdb=" N ILE A3658 " pdb=" CA ILE A3658 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.28e+00 bond pdb=" N VAL A3656 " pdb=" CA VAL A3656 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.14e-02 7.69e+03 8.00e+00 bond pdb=" N ASP A1635 " pdb=" CA ASP A1635 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.23e+00 bond pdb=" N ILE A1636 " pdb=" CA ILE A1636 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.26e-02 6.30e+03 6.98e+00 ... (remaining 21432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 28439 1.85 - 3.70: 457 3.70 - 5.56: 70 5.56 - 7.41: 17 7.41 - 9.26: 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 112.98 107.86 5.12 1.25e+00 6.40e-01 1.68e+01 angle pdb=" N LYS A3634 " pdb=" CA LYS A3634 " pdb=" C LYS A3634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.57e+01 angle pdb=" N SER A3810 " pdb=" CA SER A3810 " pdb=" C SER A3810 " ideal model delta sigma weight residual 110.80 118.73 -7.93 2.13e+00 2.20e-01 1.39e+01 angle pdb=" N GLN A1362 " pdb=" CA GLN A1362 " pdb=" CB GLN A1362 " ideal model delta sigma weight residual 110.12 115.42 -5.30 1.47e+00 4.63e-01 1.30e+01 angle pdb=" CA LYS A3660 " pdb=" C LYS A3660 " pdb=" O LYS A3660 " ideal model delta sigma weight residual 122.64 118.32 4.32 1.25e+00 6.40e-01 1.19e+01 ... (remaining 28981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 12003 21.89 - 43.78: 792 43.78 - 65.67: 113 65.67 - 87.56: 32 87.56 - 109.44: 8 Dihedral angle restraints: 12948 sinusoidal: 5357 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 180.00 139.08 40.92 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 -145.59 -34.41 0 5.00e+00 4.00e-02 4.74e+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 49.45 -109.44 1 2.00e+01 2.50e-03 3.20e+01 ... (remaining 12945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2298 0.039 - 0.077: 740 0.077 - 0.116: 196 0.116 - 0.155: 41 0.155 - 0.193: 8 Chirality restraints: 3283 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 9.36e-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 2.63 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE A1636 " pdb=" N ILE A1636 " pdb=" C ILE A1636 " pdb=" CB ILE A1636 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 3280 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2518 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A2519 " -0.102 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 3.94e+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 delta sigma weight rms_deltas residual plane pdb=" C THR A2203 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A2204 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A2204 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A2204 " -0.023 5.00e-02 4.00e+02 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 113 2.50 - 3.10: 15898 3.10 - 3.70: 32434 3.70 - 4.30: 46596 4.30 - 4.90: 78042 Nonbonded interactions: 173083 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 1.942 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 2.160 3.040 ... (remaining 173078 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: 4.180 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 21437 Z= 0.195 Angle : 0.595 9.262 28986 Z= 0.328 Chirality : 0.042 0.193 3283 Planarity : 0.004 0.059 3651 Dihedral : 14.879 109.444 8018 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.08 % Allowed : 0.47 % Favored : 99.45 % 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: 0.34 (0.17), residues: 2579 helix: 1.23 (0.13), residues: 1507 sheet: -1.27 (0.37), residues: 199 loop : -1.12 (0.20), residues: 873 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 0.00403 (21437) covalent geometry : angle 0.59534 (28986) hydrogen bonds : bond 0.13361 ( 1165) hydrogen bonds : angle 5.66913 ( 3438) *********************** 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 220 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7516 (ttm) cc_final: 0.7262 (ttm) REVERT: A 3565 ARG cc_start: 0.8042 (tpt90) cc_final: 0.7842 (tpt170) outliers start: 2 outliers final: 0 residues processed: 219 average time/residue: 0.1694 time to fit residues: 57.4616 Evaluate side-chains 170 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS A2043 GLN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 ASN A2634 ASN A3453 GLN A3596 ASN A3741 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108603 restraints weight = 32566.229| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21437 Z= 0.150 Angle : 0.555 8.173 28986 Z= 0.284 Chirality : 0.041 0.185 3283 Planarity : 0.004 0.044 3651 Dihedral : 6.065 109.146 2827 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.68 % Allowed : 5.89 % Favored : 93.43 % 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: 0.62 (0.17), residues: 2579 helix: 1.47 (0.13), residues: 1530 sheet: -1.17 (0.37), residues: 194 loop : -1.12 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2209 TYR 0.017 0.001 TYR A2571 PHE 0.024 0.001 PHE A3016 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00345 (21437) covalent geometry : angle 0.55479 (28986) hydrogen bonds : bond 0.04221 ( 1165) hydrogen bonds : angle 4.29613 ( 3438) *********************** 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 223 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7880 (ttm) cc_final: 0.7558 (ttm) REVERT: A 1359 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6200 (tm-30) REVERT: A 1468 PHE cc_start: 0.6843 (m-80) cc_final: 0.6637 (m-80) REVERT: A 2371 PHE cc_start: 0.7042 (t80) cc_final: 0.6601 (t80) REVERT: A 3556 LYS cc_start: 0.5713 (mttt) cc_final: 0.5384 (mptt) REVERT: A 3835 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7724 (tm-30) REVERT: A 4087 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 16 outliers final: 8 residues processed: 214 average time/residue: 0.1602 time to fit residues: 54.0249 Evaluate side-chains 180 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3741 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 58 optimal weight: 0.3980 chunk 221 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 HIS A3680 GLN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107959 restraints weight = 32652.116| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.15 r_work: 0.3216 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21437 Z= 0.170 Angle : 0.551 7.701 28986 Z= 0.280 Chirality : 0.040 0.171 3283 Planarity : 0.003 0.042 3651 Dihedral : 6.062 109.802 2827 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.02 % Allowed : 9.88 % Favored : 89.10 % 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: 0.67 (0.17), residues: 2579 helix: 1.53 (0.13), residues: 1532 sheet: -1.14 (0.39), residues: 184 loop : -1.15 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2412 TYR 0.017 0.001 TYR A2571 PHE 0.018 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00403 (21437) covalent geometry : angle 0.55104 (28986) hydrogen bonds : bond 0.04033 ( 1165) hydrogen bonds : angle 4.16479 ( 3438) *********************** 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 208 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7886 (ttm) cc_final: 0.7546 (ttm) REVERT: A 1362 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: A 1678 MET cc_start: 0.8335 (mmm) cc_final: 0.8089 (mtt) REVERT: A 1749 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 2371 PHE cc_start: 0.7030 (t80) cc_final: 0.6577 (t80) REVERT: A 2952 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 3556 LYS cc_start: 0.5803 (mttt) cc_final: 0.5582 (mttt) REVERT: A 3565 ARG cc_start: 0.8613 (tpt170) cc_final: 0.8026 (tpp80) REVERT: A 3568 GLU cc_start: 0.7567 (pp20) cc_final: 0.7226 (tp30) REVERT: A 3746 TYR cc_start: 0.8056 (m-80) cc_final: 0.7829 (m-80) REVERT: A 3835 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7672 (tm-30) REVERT: A 4000 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 4087 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7953 (tm-30) outliers start: 24 outliers final: 15 residues processed: 197 average time/residue: 0.1608 time to fit residues: 49.7757 Evaluate side-chains 192 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2428 MET Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3593 GLU Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3851 VAL Chi-restraints excluded: chain A residue 4000 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 68 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1709 ASN A1788 GLN ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3741 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108018 restraints weight = 32698.294| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.29 r_work: 0.3210 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21437 Z= 0.134 Angle : 0.515 7.575 28986 Z= 0.263 Chirality : 0.039 0.164 3283 Planarity : 0.003 0.040 3651 Dihedral : 5.925 107.371 2827 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 11.07 % Favored : 87.40 % 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: 0.82 (0.17), residues: 2579 helix: 1.64 (0.13), residues: 1538 sheet: -1.09 (0.38), residues: 191 loop : -1.08 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2412 TYR 0.016 0.001 TYR A2571 PHE 0.017 0.001 PHE A3798 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00310 (21437) covalent geometry : angle 0.51539 (28986) hydrogen bonds : bond 0.03678 ( 1165) hydrogen bonds : angle 3.98752 ( 3438) *********************** 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: 36 poor density : 192 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7821 (ttm) cc_final: 0.7471 (ttm) REVERT: A 1362 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: A 1749 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 2371 PHE cc_start: 0.7120 (t80) cc_final: 0.6556 (t80) REVERT: A 2952 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7004 (mt) REVERT: A 3306 TRP cc_start: 0.7674 (t60) cc_final: 0.7334 (t-100) REVERT: A 3556 LYS cc_start: 0.5773 (mttt) cc_final: 0.5479 (mptt) REVERT: A 3835 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7704 (tm-30) REVERT: A 3846 MET cc_start: 0.8682 (ptp) cc_final: 0.8385 (ptt) REVERT: A 4000 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 4087 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7882 (tm-30) outliers start: 36 outliers final: 16 residues processed: 216 average time/residue: 0.1546 time to fit residues: 52.4200 Evaluate side-chains 195 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2428 MET Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3741 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3851 VAL Chi-restraints excluded: chain A residue 4000 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 0.0570 chunk 118 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 151 optimal weight: 0.0470 chunk 220 optimal weight: 10.0000 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 HIS ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110118 restraints weight = 32352.503| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.31 r_work: 0.3240 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21437 Z= 0.105 Angle : 0.504 9.137 28986 Z= 0.254 Chirality : 0.038 0.160 3283 Planarity : 0.003 0.041 3651 Dihedral : 5.783 105.344 2827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.19 % Allowed : 12.21 % Favored : 86.60 % 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: 1.03 (0.17), residues: 2579 helix: 1.80 (0.13), residues: 1532 sheet: -0.87 (0.38), residues: 191 loop : -1.00 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2528 TYR 0.027 0.001 TYR A1421 PHE 0.016 0.001 PHE A3798 TRP 0.018 0.001 TRP A2084 HIS 0.007 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00227 (21437) covalent geometry : angle 0.50362 (28986) hydrogen bonds : bond 0.03433 ( 1165) hydrogen bonds : angle 3.89260 ( 3438) *********************** 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 223 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7881 (ttm) cc_final: 0.7494 (ttm) REVERT: A 1362 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: A 2063 MET cc_start: 0.8582 (ttm) cc_final: 0.8307 (mtt) REVERT: A 2371 PHE cc_start: 0.7117 (t80) cc_final: 0.6540 (t80) REVERT: A 2952 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 3306 TRP cc_start: 0.7697 (t60) cc_final: 0.7435 (t-100) REVERT: A 3556 LYS cc_start: 0.5855 (mttt) cc_final: 0.5587 (mttt) REVERT: A 3568 GLU cc_start: 0.7569 (pp20) cc_final: 0.7329 (tp30) REVERT: A 3835 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7732 (tm-30) REVERT: A 3843 ASN cc_start: 0.8576 (m-40) cc_final: 0.8325 (m-40) REVERT: A 4000 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 4087 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 0.1518 time to fit residues: 51.4794 Evaluate side-chains 200 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3741 ASN Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3851 VAL Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4000 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3765 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109270 restraints weight = 32354.671| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.53 r_work: 0.3243 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21437 Z= 0.124 Angle : 0.509 8.445 28986 Z= 0.257 Chirality : 0.039 0.163 3283 Planarity : 0.003 0.039 3651 Dihedral : 5.744 101.819 2827 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 13.15 % Favored : 85.33 % 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: 1.06 (0.17), residues: 2579 helix: 1.82 (0.13), residues: 1535 sheet: -0.84 (0.38), residues: 191 loop : -0.99 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1905 TYR 0.015 0.001 TYR A2571 PHE 0.019 0.001 PHE A3638 TRP 0.015 0.001 TRP A2084 HIS 0.006 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00286 (21437) covalent geometry : angle 0.50856 (28986) hydrogen bonds : bond 0.03489 ( 1165) hydrogen bonds : angle 3.86239 ( 3438) *********************** 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 223 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7866 (ttm) cc_final: 0.7485 (ttm) REVERT: A 1362 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: A 1421 TYR cc_start: 0.8176 (t80) cc_final: 0.7904 (t80) REVERT: A 1749 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 2371 PHE cc_start: 0.7109 (t80) cc_final: 0.6520 (t80) REVERT: A 2952 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6984 (mt) REVERT: A 3306 TRP cc_start: 0.7833 (t60) cc_final: 0.7586 (t-100) REVERT: A 3556 LYS cc_start: 0.5865 (mttt) cc_final: 0.5634 (mptt) REVERT: A 3835 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7811 (tm-30) REVERT: A 4000 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 4087 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7566 (tm-30) outliers start: 36 outliers final: 19 residues processed: 212 average time/residue: 0.1399 time to fit residues: 47.4764 Evaluate side-chains 205 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3851 VAL Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4000 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 90 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 189 optimal weight: 0.5980 chunk 179 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1709 ASN A1891 HIS A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111418 restraints weight = 32558.257| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.30 r_work: 0.3260 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21437 Z= 0.098 Angle : 0.507 11.653 28986 Z= 0.251 Chirality : 0.038 0.176 3283 Planarity : 0.003 0.046 3651 Dihedral : 5.592 96.614 2827 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.40 % Allowed : 13.61 % Favored : 84.99 % 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: 1.22 (0.17), residues: 2579 helix: 1.95 (0.13), residues: 1538 sheet: -0.74 (0.38), residues: 191 loop : -0.95 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2412 TYR 0.012 0.001 TYR A2571 PHE 0.019 0.001 PHE A2094 TRP 0.014 0.001 TRP A2084 HIS 0.007 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00213 (21437) covalent geometry : angle 0.50722 (28986) hydrogen bonds : bond 0.03225 ( 1165) hydrogen bonds : angle 3.77190 ( 3438) *********************** 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 237 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1284 MET cc_start: -0.1067 (mtm) cc_final: -0.1364 (mtm) REVERT: A 1317 MET cc_start: 0.7882 (ttm) cc_final: 0.7501 (ttm) REVERT: A 1359 GLU cc_start: 0.6323 (tm-30) cc_final: 0.5985 (tm-30) REVERT: A 1362 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: A 1421 TYR cc_start: 0.8109 (t80) cc_final: 0.7803 (t80) REVERT: A 1749 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 1829 GLN cc_start: 0.7852 (tp40) cc_final: 0.7610 (tp40) REVERT: A 2371 PHE cc_start: 0.7289 (t80) cc_final: 0.6648 (t80) REVERT: A 2805 ASP cc_start: 0.8132 (m-30) cc_final: 0.7915 (m-30) REVERT: A 2952 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7185 (mt) REVERT: A 3746 TYR cc_start: 0.8082 (m-80) cc_final: 0.7845 (m-80) REVERT: A 3835 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7819 (tm-30) REVERT: A 4000 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 4087 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7552 (tm-30) outliers start: 33 outliers final: 15 residues processed: 227 average time/residue: 0.1513 time to fit residues: 54.8054 Evaluate side-chains 205 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3698 MET Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4000 GLU Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 55 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1629 GLN ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 ASN A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2832 ASN A3780 ASN A3843 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3988 HIS A4013 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104597 restraints weight = 32529.134| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.41 r_work: 0.3183 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21437 Z= 0.253 Angle : 0.623 13.125 28986 Z= 0.312 Chirality : 0.044 0.263 3283 Planarity : 0.004 0.045 3651 Dihedral : 5.937 89.442 2827 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.31 % Allowed : 13.95 % Favored : 84.73 % 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: 0.76 (0.17), residues: 2579 helix: 1.56 (0.13), residues: 1538 sheet: -1.01 (0.38), residues: 191 loop : -1.06 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3565 TYR 0.022 0.002 TYR A2571 PHE 0.021 0.002 PHE A2094 TRP 0.030 0.002 TRP A3306 HIS 0.007 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00615 (21437) covalent geometry : angle 0.62320 (28986) hydrogen bonds : bond 0.04156 ( 1165) hydrogen bonds : angle 4.12194 ( 3438) *********************** 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 221 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1362 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: A 1363 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7783 (mmmt) REVERT: A 1421 TYR cc_start: 0.8207 (t80) cc_final: 0.7988 (t80) REVERT: A 2322 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 2371 PHE cc_start: 0.7152 (t80) cc_final: 0.6578 (t80) REVERT: A 2805 ASP cc_start: 0.8112 (m-30) cc_final: 0.7896 (m-30) REVERT: A 3345 MET cc_start: 0.8623 (mmp) cc_final: 0.8342 (mmm) REVERT: A 3351 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7819 (ptp-110) REVERT: A 3556 LYS cc_start: 0.5776 (mttt) cc_final: 0.5529 (mttt) REVERT: A 3568 GLU cc_start: 0.7739 (pp20) cc_final: 0.7364 (tp30) REVERT: A 3595 MET cc_start: 0.7709 (mtm) cc_final: 0.7443 (ptp) REVERT: A 3835 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7800 (tm-30) REVERT: A 3873 MET cc_start: 0.8475 (tpp) cc_final: 0.7943 (tpt) REVERT: A 4087 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 31 outliers final: 20 residues processed: 211 average time/residue: 0.1454 time to fit residues: 48.1679 Evaluate side-chains 204 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2322 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3351 ARG Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 126 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS A1979 ASN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2832 ASN A2886 HIS ** A3596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109499 restraints weight = 32331.488| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.13 r_work: 0.3245 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21437 Z= 0.122 Angle : 0.561 14.142 28986 Z= 0.275 Chirality : 0.039 0.227 3283 Planarity : 0.003 0.048 3651 Dihedral : 5.747 82.951 2827 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.19 % Allowed : 14.63 % Favored : 84.18 % 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: 0.95 (0.17), residues: 2579 helix: 1.73 (0.13), residues: 1544 sheet: -0.94 (0.38), residues: 191 loop : -1.04 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2412 TYR 0.024 0.001 TYR A3785 PHE 0.021 0.001 PHE A3798 TRP 0.040 0.001 TRP A3306 HIS 0.007 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00276 (21437) covalent geometry : angle 0.56063 (28986) hydrogen bonds : bond 0.03574 ( 1165) hydrogen bonds : angle 3.92836 ( 3438) *********************** 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 210 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1317 MET cc_start: 0.7847 (ttm) cc_final: 0.7489 (ttm) REVERT: A 1362 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: A 1678 MET cc_start: 0.8533 (mmm) cc_final: 0.8182 (mtt) REVERT: A 2371 PHE cc_start: 0.7309 (t80) cc_final: 0.6664 (t80) REVERT: A 2797 MET cc_start: 0.8668 (tpp) cc_final: 0.8433 (tpp) REVERT: A 2805 ASP cc_start: 0.8464 (m-30) cc_final: 0.8227 (m-30) REVERT: A 2952 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 3351 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (ptp-110) REVERT: A 3556 LYS cc_start: 0.5504 (mttt) cc_final: 0.5260 (mptt) REVERT: A 3568 GLU cc_start: 0.7812 (pp20) cc_final: 0.7530 (tp30) REVERT: A 3595 MET cc_start: 0.7848 (mtm) cc_final: 0.7546 (ptp) REVERT: A 3835 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7826 (tm-30) REVERT: A 3873 MET cc_start: 0.8548 (tpp) cc_final: 0.8267 (tpt) REVERT: A 4000 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 4087 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7578 (tm-30) outliers start: 28 outliers final: 21 residues processed: 202 average time/residue: 0.1418 time to fit residues: 45.8284 Evaluate side-chains 200 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3351 ARG Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3733 VAL Chi-restraints excluded: chain A residue 3741 ASN Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4000 GLU Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 15 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2832 ASN A3484 HIS ** A3596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105943 restraints weight = 32589.133| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.27 r_work: 0.3181 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21437 Z= 0.187 Angle : 0.596 14.142 28986 Z= 0.294 Chirality : 0.042 0.212 3283 Planarity : 0.003 0.057 3651 Dihedral : 5.795 75.955 2827 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.36 % Allowed : 14.63 % Favored : 84.01 % 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: 0.81 (0.17), residues: 2579 helix: 1.60 (0.13), residues: 1543 sheet: -1.05 (0.39), residues: 185 loop : -1.05 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2412 TYR 0.019 0.001 TYR A2571 PHE 0.023 0.002 PHE A3798 TRP 0.034 0.001 TRP A3306 HIS 0.008 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00449 (21437) covalent geometry : angle 0.59563 (28986) hydrogen bonds : bond 0.03858 ( 1165) hydrogen bonds : angle 4.03079 ( 3438) ********************** 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 209 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1362 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: A 2322 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 2371 PHE cc_start: 0.7185 (t80) cc_final: 0.6631 (t80) REVERT: A 2805 ASP cc_start: 0.8150 (m-30) cc_final: 0.7930 (m-30) REVERT: A 3351 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7883 (ptp-110) REVERT: A 3556 LYS cc_start: 0.5745 (mttt) cc_final: 0.5468 (mptt) REVERT: A 3568 GLU cc_start: 0.7858 (pp20) cc_final: 0.7602 (tp30) REVERT: A 3595 MET cc_start: 0.7761 (mtm) cc_final: 0.7456 (ptp) REVERT: A 3873 MET cc_start: 0.8548 (tpp) cc_final: 0.8286 (tpt) REVERT: A 4000 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 4087 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 4090 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7901 (mm-40) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 0.1593 time to fit residues: 50.9471 Evaluate side-chains 200 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1400 VAL Chi-restraints excluded: chain A residue 1569 ILE Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2133 ILE Chi-restraints excluded: chain A residue 2322 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2782 VAL Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3351 ARG Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3400 SER Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3613 ASN Chi-restraints excluded: chain A residue 3733 VAL Chi-restraints excluded: chain A residue 3741 ASN Chi-restraints excluded: chain A residue 3895 PHE Chi-restraints excluded: chain A residue 4000 GLU Chi-restraints excluded: chain A residue 4023 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 255 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 202 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107891 restraints weight = 32526.901| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.46 r_work: 0.3226 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21437 Z= 0.126 Angle : 0.555 14.708 28986 Z= 0.273 Chirality : 0.040 0.217 3283 Planarity : 0.003 0.053 3651 Dihedral : 5.652 69.532 2827 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.31 % Allowed : 14.63 % Favored : 84.05 % 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: 1.00 (0.17), residues: 2579 helix: 1.78 (0.13), residues: 1538 sheet: -1.20 (0.37), residues: 195 loop : -0.94 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2412 TYR 0.016 0.001 TYR A3785 PHE 0.023 0.001 PHE A3798 TRP 0.040 0.001 TRP A3306 HIS 0.005 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00291 (21437) covalent geometry : angle 0.55465 (28986) hydrogen bonds : bond 0.03520 ( 1165) hydrogen bonds : angle 3.90118 ( 3438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4688.44 seconds wall clock time: 81 minutes 36.86 seconds (4896.86 seconds total)