Starting phenix.real_space_refine on Fri Feb 6 10:58:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.map" model { file = "/net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mfy_48242/02_2026/9mfy_48242.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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 2 5.21 5 S 114 5.16 5 C 15303 2.51 5 N 3995 2.21 5 O 4471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 23892 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2880 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 339} 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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.92, per 1000 atoms: 0.21 Number of scatterers: 23892 At special positions: 0 Unit cell: (111.101, 153.921, 182.853, 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 114 16.00 P 7 15.00 Mg 2 11.99 O 4471 8.00 N 3995 7.00 C 15303 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: 2.02 Conformation dependent library (CDL) restraints added in 943.9 milliseconds 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 23 sheets defined 57.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'A' and resid 1242 through 1250 Processing helix chain 'A' and resid 1252 through 1256 removed outlier: 3.705A pdb=" N VAL A1256 " --> pdb=" O TRP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1274 removed outlier: 3.646A pdb=" N ASP A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A1274 " --> pdb=" O ARG A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 3.767A pdb=" N LYS A1286 " --> pdb=" O PHE A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1328 through 1334 removed outlier: 3.609A pdb=" N LYS A1334 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1345 removed outlier: 3.610A pdb=" N LEU A1345 " --> pdb=" O ASP A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1379 removed outlier: 4.820A pdb=" N ILE A1367 " --> pdb=" O LYS A1363 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1416 removed outlier: 3.537A pdb=" N GLU A1402 " --> pdb=" O TRP A1398 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1422 removed outlier: 6.005A pdb=" N TYR A1420 " --> pdb=" O ALA A1417 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A1422 " --> pdb=" O ASN A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1459 removed outlier: 3.697A pdb=" N ASN A1444 " --> pdb=" O GLU A1440 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 3.788A 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: 3.602A pdb=" N GLN A1492 " --> pdb=" O THR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1502 removed outlier: 3.536A pdb=" N ILE A1500 " --> pdb=" O ILE A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1534 Processing helix chain 'A' and resid 1535 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1556 through 1560 removed outlier: 3.699A pdb=" N SER A1559 " --> pdb=" O ASP A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1631 removed outlier: 3.581A pdb=" N THR A1613 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.743A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1667 Processing helix chain 'A' and resid 1668 through 1689 removed outlier: 4.080A pdb=" N TYR A1672 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1718 removed outlier: 3.700A pdb=" N VAL A1703 " --> pdb=" O GLU A1699 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.619A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.903A 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: 3.860A 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 1911 through 1914 removed outlier: 3.719A pdb=" N LYS A1914 " --> pdb=" O ASN A1911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1911 through 1914' Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1987 removed outlier: 4.130A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 4.349A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2002 removed outlier: 3.797A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2007 through 2022 removed outlier: 3.985A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A2013 " --> pdb=" O THR A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2046 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 3.743A pdb=" N LYS A2065 " --> pdb=" O TYR A2061 " (cutoff:3.500A) removed outlier: 4.458A 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 2144 through 2146 No H-bonds generated for 'chain 'A' and resid 2144 through 2146' Processing helix chain 'A' and resid 2159 through 2165 removed outlier: 3.905A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2210 removed outlier: 3.514A pdb=" N ILE A2207 " --> pdb=" O THR A2203 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2238 Processing helix chain 'A' and resid 2242 through 2257 removed outlier: 3.687A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2271 removed outlier: 4.649A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2297 removed outlier: 5.063A pdb=" N GLU A2285 " --> pdb=" O PHE A2281 " (cutoff:3.500A) removed outlier: 4.415A 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 2331 through 2346 Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.608A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.983A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2462 removed outlier: 3.960A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A2461 " --> pdb=" O ALA A2457 " (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 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.111A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.506A pdb=" N ALA A2593 " --> pdb=" O THR A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.868A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2656 Processing helix chain 'A' and resid 2663 through 2681 Processing helix chain 'A' and resid 2690 through 2694 removed outlier: 3.743A pdb=" N LEU A2694 " --> pdb=" O SER A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.575A pdb=" N THR A2722 " --> pdb=" O GLU A2718 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2778 Processing helix chain 'A' and resid 2791 through 2809 removed outlier: 3.824A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A2809 " --> pdb=" O ASP A2805 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.585A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A2837 " --> pdb=" O THR A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 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 2935 through 2939 Processing helix chain 'A' and resid 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2981 removed outlier: 3.629A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A2981 " --> pdb=" O TYR A2977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3027 Processing helix chain 'A' and resid 3298 through 3308 removed outlier: 3.607A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3310 through 3317 Processing helix chain 'A' and resid 3319 through 3333 Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 3.634A 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 3357 Processing helix chain 'A' and resid 3365 through 3371 removed outlier: 3.731A pdb=" N LEU A3370 " --> pdb=" O PHE A3366 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A3371 " --> pdb=" O ILE A3367 " (cutoff:3.500A) Processing helix chain 'A' and resid 3372 through 3382 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.131A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (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 3446 removed outlier: 4.093A pdb=" N ARG A3445 " --> pdb=" O GLU A3441 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A3446 " --> pdb=" O ASN A3442 " (cutoff:3.500A) Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.592A pdb=" N SER A3467 " --> pdb=" O SER A3463 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3513 Processing helix chain 'A' and resid 3525 through 3538 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 4.080A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A3572 " --> pdb=" O GLU A3568 " (cutoff:3.500A) Processing helix chain 'A' and resid 3576 through 3581 removed outlier: 3.612A pdb=" N ASP A3581 " --> pdb=" O MET A3577 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3639 Proline residue: A3609 - end of helix removed outlier: 4.664A pdb=" N GLU A3616 " --> pdb=" O ASP A3612 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLU A3617 " --> pdb=" O ASN A3613 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR A3618 " --> pdb=" O LEU A3614 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 4.167A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.594A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.907A 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: 3.981A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3741 through 3753 removed outlier: 3.572A pdb=" N ARG A3745 " --> pdb=" O ASN A3741 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A3746 " --> pdb=" O ASN A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.378A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.502A 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 3807 Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 3.999A pdb=" N SER A3830 " --> pdb=" O GLN A3826 " (cutoff:3.500A) removed outlier: 3.695A 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: 4.120A 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 3943 removed outlier: 3.726A pdb=" N VAL A3926 " --> pdb=" O GLY A3922 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.965A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 removed outlier: 3.542A pdb=" N ASP A3987 " --> pdb=" O ALA A3983 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4016 removed outlier: 3.557A pdb=" N CYS A4016 " --> pdb=" O ALA A4012 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4092 Processing sheet with id=AA1, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 163 removed outlier: 4.272A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 174 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 192 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208 removed outlier: 4.495A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 263 removed outlier: 3.508A pdb=" N LYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 304 through 306 removed outlier: 6.248A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 346 removed outlier: 3.559A pdb=" N LYS B 342 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR B 372 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 383 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 377 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 391 through 393 removed outlier: 3.667A pdb=" N ILE B 399 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET B 393 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA B 397 " --> pdb=" O MET B 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 420 through 426 removed outlier: 6.316A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1384 through 1387 removed outlier: 4.349A pdb=" N GLU A1384 " --> pdb=" O ARG A1396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1569 through 1575 removed outlier: 6.219A pdb=" N ILE A1569 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER A1584 " --> pdb=" O ILE A1569 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A1571 " --> pdb=" O VAL A1582 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL A1582 " --> pdb=" O SER A1571 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A1573 " --> pdb=" O THR A1580 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N PHE A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLU A1594 " --> pdb=" O PHE A1578 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AB3, first strand: chain 'A' and resid 1818 through 1819 removed outlier: 6.438A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A1917 " --> pdb=" O GLY A1791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AB5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.867A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AB7, first strand: chain 'A' and resid 2438 through 2440 Processing sheet with id=AB8, first strand: chain 'A' and resid 2438 through 2440 removed outlier: 7.105A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2465 through 2466 removed outlier: 4.183A pdb=" N THR A2472 " --> pdb=" O TRP A2523 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.913A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.284A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 3427 through 3429 removed outlier: 6.397A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 3471 through 3472 removed outlier: 3.590A pdb=" N THR A3478 " --> pdb=" O ASN A3471 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 6.436A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR A3787 " --> pdb=" O PHE A3895 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A3897 " --> pdb=" O THR A3787 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA A3789 " --> pdb=" O TYR A3897 " (cutoff:3.500A) 1285 hydrogen bonds defined for protein. 3747 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: 6.70 Time building geometry restraints manager: 2.67 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: 7670 1.34 - 1.46: 5449 1.46 - 1.58: 11092 1.58 - 1.70: 7 1.70 - 1.82: 180 Bond restraints: 24398 Sorted by residual: bond pdb=" N VAL A3656 " pdb=" CA VAL A3656 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.17e-02 7.31e+03 9.52e+00 bond pdb=" N ILE A2961 " pdb=" CA ILE A2961 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N ILE A2958 " pdb=" CA ILE A2958 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 7.93e+00 bond pdb=" N PHE A3356 " pdb=" CA PHE A3356 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.32e-02 5.74e+03 7.87e+00 bond pdb=" N ILE A3658 " pdb=" CA ILE A3658 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.74e+00 ... (remaining 24393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 32665 2.58 - 5.16: 308 5.16 - 7.74: 38 7.74 - 10.32: 3 10.32 - 12.90: 1 Bond angle restraints: 33015 Sorted by residual: angle pdb=" C SER A2563 " pdb=" CA SER A2563 " pdb=" CB SER A2563 " ideal model delta sigma weight residual 115.79 109.21 6.58 1.19e+00 7.06e-01 3.06e+01 angle pdb=" CA ILE A2944 " pdb=" C ILE A2944 " pdb=" O ILE A2944 " ideal model delta sigma weight residual 122.63 118.46 4.17 8.70e-01 1.32e+00 2.30e+01 angle pdb=" C PHE A3356 " pdb=" CA PHE A3356 " pdb=" CB PHE A3356 " ideal model delta sigma weight residual 109.29 116.29 -7.00 1.82e+00 3.02e-01 1.48e+01 angle pdb=" CA GLU A2947 " pdb=" C GLU A2947 " pdb=" O GLU A2947 " ideal model delta sigma weight residual 120.63 116.53 4.10 1.08e+00 8.57e-01 1.44e+01 angle pdb=" N PHE A3356 " pdb=" CA PHE A3356 " pdb=" C PHE A3356 " ideal model delta sigma weight residual 113.50 108.96 4.54 1.23e+00 6.61e-01 1.36e+01 ... (remaining 33010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13230 17.97 - 35.93: 1168 35.93 - 53.90: 173 53.90 - 71.87: 82 71.87 - 89.83: 38 Dihedral angle restraints: 14691 sinusoidal: 6057 harmonic: 8634 Sorted by residual: dihedral pdb=" CA PHE A1282 " pdb=" C PHE A1282 " pdb=" N GLU A1283 " pdb=" CA GLU A1283 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN A2837 " pdb=" C ASN A2837 " pdb=" N ALA A2838 " pdb=" CA ALA A2838 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA SER A1825 " pdb=" C SER A1825 " pdb=" N PHE A1826 " pdb=" CA PHE A1826 " ideal model delta harmonic sigma weight residual -180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 14688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2663 0.040 - 0.080: 782 0.080 - 0.121: 240 0.121 - 0.161: 39 0.161 - 0.201: 8 Chirality restraints: 3732 Sorted by residual: chirality pdb=" CA ILE A3658 " pdb=" N ILE A3658 " pdb=" C ILE A3658 " pdb=" CB ILE A3658 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A2944 " pdb=" N ILE A2944 " pdb=" C ILE A2944 " pdb=" CB ILE A2944 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA VAL A2945 " pdb=" N VAL A2945 " pdb=" C VAL A2945 " pdb=" CB VAL A2945 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 3729 not shown) Planarity restraints: 4157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2474 " 0.054 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A2475 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A2475 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A2475 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A2939 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C GLU A2939 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU A2939 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A2940 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A3583 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C LEU A3583 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A3583 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A3584 " -0.011 2.00e-02 2.50e+03 ... (remaining 4154 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 1 2.12 - 2.81: 6638 2.81 - 3.51: 34831 3.51 - 4.20: 55234 4.20 - 4.90: 100903 Nonbonded interactions: 197607 Sorted by model distance: nonbonded pdb=" CB THR A2081 " pdb="MG MG A4105 " model vdw 1.419 2.600 nonbonded pdb=" OE1 GLU A2195 " pdb="MG MG A4105 " model vdw 2.116 2.170 nonbonded pdb=" OE2 GLU A2195 " pdb="MG MG A4105 " model vdw 2.122 2.170 nonbonded pdb=" O SER A3524 " pdb=" N GLU A3526 " model vdw 2.128 3.120 nonbonded pdb=" O TRP A3306 " pdb=" OG1 THR A3309 " model vdw 2.131 3.040 ... (remaining 197602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.150 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.058 24398 Z= 0.197 Angle : 0.622 12.898 33015 Z= 0.340 Chirality : 0.043 0.201 3732 Planarity : 0.003 0.083 4157 Dihedral : 14.883 89.832 9081 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 0.11 % Allowed : 0.26 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2933 helix: 1.72 (0.13), residues: 1512 sheet: -0.68 (0.29), residues: 341 loop : -0.98 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3351 TYR 0.018 0.001 TYR A2571 PHE 0.031 0.002 PHE A1289 TRP 0.029 0.002 TRP A3762 HIS 0.007 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00405 (24398) covalent geometry : angle 0.62213 (33015) hydrogen bonds : bond 0.13988 ( 1283) hydrogen bonds : angle 5.71229 ( 3747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 325 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ILE cc_start: 0.8717 (mp) cc_final: 0.8323 (mt) REVERT: B 493 MET cc_start: 0.7428 (mtm) cc_final: 0.7021 (mtm) REVERT: A 1329 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8011 (tptp) REVERT: A 1367 ILE cc_start: 0.8462 (mt) cc_final: 0.8154 (mt) REVERT: A 1741 LEU cc_start: 0.7382 (tp) cc_final: 0.6999 (tt) REVERT: A 1784 ASP cc_start: 0.8182 (t70) cc_final: 0.7891 (t0) REVERT: A 2118 MET cc_start: 0.7780 (tpt) cc_final: 0.7412 (ttm) REVERT: A 2180 ASN cc_start: 0.7915 (p0) cc_final: 0.7499 (p0) REVERT: A 2426 MET cc_start: 0.7263 (tmm) cc_final: 0.6890 (tmm) REVERT: A 2428 MET cc_start: 0.7692 (tmm) cc_final: 0.7341 (tmm) REVERT: A 3320 LEU cc_start: 0.7604 (tt) cc_final: 0.7389 (tp) REVERT: A 3324 CYS cc_start: 0.7551 (m) cc_final: 0.7299 (m) REVERT: A 4089 LEU cc_start: 0.7929 (mt) cc_final: 0.7021 (mm) outliers start: 3 outliers final: 1 residues processed: 327 average time/residue: 0.1590 time to fit residues: 82.2948 Evaluate side-chains 262 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2960 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1466 GLN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1979 ASN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2598 HIS A2787 HIS ** A2858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2927 GLN A3318 GLN A3637 GLN A3714 GLN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3975 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096455 restraints weight = 40263.273| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.82 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24398 Z= 0.136 Angle : 0.575 11.618 33015 Z= 0.292 Chirality : 0.042 0.192 3732 Planarity : 0.003 0.048 4157 Dihedral : 5.782 75.256 3209 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 0.89 % Allowed : 7.55 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2933 helix: 1.83 (0.13), residues: 1533 sheet: -0.61 (0.29), residues: 340 loop : -0.95 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2962 TYR 0.016 0.001 TYR A3007 PHE 0.021 0.001 PHE A3313 TRP 0.022 0.001 TRP A2084 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00308 (24398) covalent geometry : angle 0.57467 (33015) hydrogen bonds : bond 0.03925 ( 1283) hydrogen bonds : angle 4.32223 ( 3747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7155 (t0) cc_final: 0.6895 (t0) REVERT: B 493 MET cc_start: 0.8183 (mtm) cc_final: 0.7763 (mtm) REVERT: A 1329 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7814 (tptp) REVERT: A 1367 ILE cc_start: 0.8548 (mt) cc_final: 0.8241 (mt) REVERT: A 1741 LEU cc_start: 0.7420 (tp) cc_final: 0.7165 (tt) REVERT: A 1784 ASP cc_start: 0.8635 (t70) cc_final: 0.8362 (t0) REVERT: A 2091 MET cc_start: 0.8972 (mtp) cc_final: 0.8771 (mtp) REVERT: A 2180 ASN cc_start: 0.7984 (p0) cc_final: 0.7606 (p0) REVERT: A 2426 MET cc_start: 0.7960 (tmm) cc_final: 0.7751 (tmm) REVERT: A 2428 MET cc_start: 0.8116 (tmm) cc_final: 0.7592 (tmm) REVERT: A 2476 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5728 (mtmm) REVERT: A 2573 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 2962 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7441 (ttm110) REVERT: A 3007 TYR cc_start: 0.6910 (t80) cc_final: 0.6677 (t80) REVERT: A 3320 LEU cc_start: 0.7244 (tt) cc_final: 0.6985 (tp) REVERT: A 3324 CYS cc_start: 0.8693 (m) cc_final: 0.8378 (m) REVERT: A 3528 ARG cc_start: 0.6726 (mmt-90) cc_final: 0.6243 (mmt-90) REVERT: A 3595 MET cc_start: 0.7534 (mmp) cc_final: 0.6958 (tpt) outliers start: 24 outliers final: 12 residues processed: 314 average time/residue: 0.1471 time to fit residues: 73.6968 Evaluate side-chains 277 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3882 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 98 optimal weight: 0.2980 chunk 232 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2858 ASN A3561 ASN A3714 GLN ** A3845 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.134446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093663 restraints weight = 40076.981| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.84 r_work: 0.3131 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24398 Z= 0.144 Angle : 0.555 11.503 33015 Z= 0.281 Chirality : 0.041 0.284 3732 Planarity : 0.003 0.048 4157 Dihedral : 5.756 73.603 3208 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 1.30 % Allowed : 9.90 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2933 helix: 1.86 (0.13), residues: 1530 sheet: -0.57 (0.29), residues: 335 loop : -0.93 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 494 TYR 0.023 0.001 TYR A3007 PHE 0.028 0.001 PHE A1289 TRP 0.036 0.001 TRP A3762 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00336 (24398) covalent geometry : angle 0.55520 (33015) hydrogen bonds : bond 0.03730 ( 1283) hydrogen bonds : angle 4.13050 ( 3747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7208 (t0) cc_final: 0.6909 (t0) REVERT: B 493 MET cc_start: 0.7930 (mtm) cc_final: 0.7520 (mtm) REVERT: A 1329 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8274 (tmtt) REVERT: A 1784 ASP cc_start: 0.8664 (t70) cc_final: 0.8382 (t0) REVERT: A 1826 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6649 (t80) REVERT: A 2247 ASP cc_start: 0.7487 (p0) cc_final: 0.7218 (t0) REVERT: A 2259 MET cc_start: 0.8102 (mmm) cc_final: 0.7797 (mmm) REVERT: A 2428 MET cc_start: 0.8136 (tmm) cc_final: 0.7579 (tmm) REVERT: A 2476 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.5670 (mtmm) REVERT: A 2661 VAL cc_start: 0.8295 (t) cc_final: 0.8016 (m) REVERT: A 2740 ASP cc_start: 0.8580 (t0) cc_final: 0.8258 (t0) REVERT: A 2962 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7455 (ttm-80) REVERT: A 3320 LEU cc_start: 0.7283 (tt) cc_final: 0.7001 (tp) REVERT: A 3324 CYS cc_start: 0.8724 (m) cc_final: 0.8439 (m) REVERT: A 3595 MET cc_start: 0.7528 (mmp) cc_final: 0.6955 (tpt) REVERT: A 4092 MET cc_start: 0.4525 (mmm) cc_final: 0.3794 (mmp) outliers start: 35 outliers final: 20 residues processed: 296 average time/residue: 0.1481 time to fit residues: 70.5851 Evaluate side-chains 278 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1826 PHE Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2354 SER Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3587 LEU Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 6 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 GLN A1717 ASN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 HIS ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 GLN A3741 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092172 restraints weight = 39948.653| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.83 r_work: 0.3111 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24398 Z= 0.165 Angle : 0.568 9.942 33015 Z= 0.286 Chirality : 0.042 0.327 3732 Planarity : 0.003 0.048 4157 Dihedral : 5.841 74.090 3208 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 1.75 % Allowed : 11.76 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2933 helix: 1.85 (0.13), residues: 1533 sheet: -0.69 (0.29), residues: 326 loop : -0.94 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2586 TYR 0.024 0.001 TYR A3007 PHE 0.028 0.002 PHE A1289 TRP 0.024 0.001 TRP A2084 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00391 (24398) covalent geometry : angle 0.56774 (33015) hydrogen bonds : bond 0.03723 ( 1283) hydrogen bonds : angle 4.06205 ( 3747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7222 (t0) cc_final: 0.6909 (t0) REVERT: B 493 MET cc_start: 0.8262 (mtm) cc_final: 0.7794 (mtm) REVERT: A 1329 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8279 (tmtt) REVERT: A 1655 MET cc_start: 0.8593 (mmm) cc_final: 0.8330 (mmt) REVERT: A 1784 ASP cc_start: 0.8695 (t70) cc_final: 0.8366 (t0) REVERT: A 1826 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6759 (t80) REVERT: A 2119 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 2180 ASN cc_start: 0.7987 (p0) cc_final: 0.7697 (p0) REVERT: A 2247 ASP cc_start: 0.7477 (p0) cc_final: 0.7220 (t0) REVERT: A 2259 MET cc_start: 0.8051 (mmm) cc_final: 0.7740 (mmm) REVERT: A 2428 MET cc_start: 0.8167 (tmm) cc_final: 0.7660 (tmm) REVERT: A 2476 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6185 (mtmm) REVERT: A 2740 ASP cc_start: 0.8614 (t0) cc_final: 0.8280 (t0) REVERT: A 2829 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 2831 MET cc_start: 0.8585 (mmm) cc_final: 0.8363 (mmp) REVERT: A 2962 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7439 (ttm110) REVERT: A 3320 LEU cc_start: 0.7268 (tt) cc_final: 0.6956 (tp) REVERT: A 3324 CYS cc_start: 0.8708 (m) cc_final: 0.8417 (m) REVERT: A 3401 GLN cc_start: 0.6194 (tp40) cc_final: 0.5507 (tm-30) REVERT: A 3595 MET cc_start: 0.7405 (mmp) cc_final: 0.6851 (tpt) outliers start: 47 outliers final: 28 residues processed: 300 average time/residue: 0.1731 time to fit residues: 81.7705 Evaluate side-chains 288 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1826 PHE Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2354 SER Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 257 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 285 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN A1667 ASN A1788 GLN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2430 ASN ** A2959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3542 GLN A3561 ASN ** A3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092670 restraints weight = 39820.258| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.83 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24398 Z= 0.148 Angle : 0.558 8.991 33015 Z= 0.279 Chirality : 0.042 0.307 3732 Planarity : 0.003 0.068 4157 Dihedral : 5.829 73.473 3208 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 1.94 % Allowed : 12.28 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2933 helix: 1.87 (0.13), residues: 1534 sheet: -0.68 (0.29), residues: 327 loop : -0.92 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2528 TYR 0.040 0.001 TYR A3007 PHE 0.029 0.001 PHE A1289 TRP 0.023 0.001 TRP A2084 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00348 (24398) covalent geometry : angle 0.55755 (33015) hydrogen bonds : bond 0.03604 ( 1283) hydrogen bonds : angle 4.00197 ( 3747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7219 (t0) cc_final: 0.6901 (t0) REVERT: B 493 MET cc_start: 0.8194 (mtm) cc_final: 0.7714 (mtm) REVERT: A 1265 LEU cc_start: 0.8261 (mm) cc_final: 0.7502 (pp) REVERT: A 1329 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8281 (tmtt) REVERT: A 1367 ILE cc_start: 0.8394 (mt) cc_final: 0.8109 (mt) REVERT: A 1655 MET cc_start: 0.8575 (mmm) cc_final: 0.8366 (mmt) REVERT: A 1741 LEU cc_start: 0.7542 (tp) cc_final: 0.7305 (tt) REVERT: A 1784 ASP cc_start: 0.8707 (t70) cc_final: 0.8368 (t0) REVERT: A 1826 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6863 (t80) REVERT: A 2247 ASP cc_start: 0.7541 (p0) cc_final: 0.7214 (t0) REVERT: A 2259 MET cc_start: 0.8092 (mmm) cc_final: 0.7747 (mmm) REVERT: A 2428 MET cc_start: 0.8147 (tmm) cc_final: 0.7677 (tmm) REVERT: A 2740 ASP cc_start: 0.8591 (t0) cc_final: 0.8256 (t0) REVERT: A 2962 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7445 (ttm-80) REVERT: A 3320 LEU cc_start: 0.7290 (tt) cc_final: 0.6999 (tp) REVERT: A 3324 CYS cc_start: 0.8723 (m) cc_final: 0.8409 (m) REVERT: A 3401 GLN cc_start: 0.6067 (tp40) cc_final: 0.5522 (tm-30) REVERT: A 3518 PHE cc_start: 0.7969 (m-80) cc_final: 0.7745 (m-80) REVERT: A 3542 GLN cc_start: 0.7745 (mt0) cc_final: 0.7317 (mt0) REVERT: A 3595 MET cc_start: 0.7420 (mmp) cc_final: 0.6838 (tpt) REVERT: A 3767 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4588 (t80) REVERT: A 3769 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6680 (m) outliers start: 52 outliers final: 31 residues processed: 294 average time/residue: 0.1637 time to fit residues: 76.4866 Evaluate side-chains 282 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1826 PHE Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2354 SER Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 169 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.090223 restraints weight = 39910.475| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.82 r_work: 0.3082 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24398 Z= 0.211 Angle : 0.607 12.397 33015 Z= 0.305 Chirality : 0.043 0.289 3732 Planarity : 0.004 0.061 4157 Dihedral : 6.120 82.177 3208 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 2.12 % Allowed : 13.03 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2933 helix: 1.75 (0.13), residues: 1538 sheet: -0.87 (0.29), residues: 323 loop : -0.99 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2528 TYR 0.019 0.002 TYR A1705 PHE 0.031 0.002 PHE A1289 TRP 0.027 0.002 TRP B 299 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00506 (24398) covalent geometry : angle 0.60711 (33015) hydrogen bonds : bond 0.03881 ( 1283) hydrogen bonds : angle 4.09646 ( 3747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7364 (t0) cc_final: 0.7109 (t0) REVERT: B 493 MET cc_start: 0.8354 (mtm) cc_final: 0.7938 (mtm) REVERT: B 494 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6572 (tmm-80) REVERT: A 1329 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8311 (tmtt) REVERT: A 1367 ILE cc_start: 0.8463 (mt) cc_final: 0.8168 (mt) REVERT: A 1741 LEU cc_start: 0.7523 (tp) cc_final: 0.7306 (tt) REVERT: A 1784 ASP cc_start: 0.8824 (t70) cc_final: 0.8424 (t0) REVERT: A 1826 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6940 (t80) REVERT: A 1841 ILE cc_start: 0.8950 (tp) cc_final: 0.8738 (tp) REVERT: A 2247 ASP cc_start: 0.7565 (p0) cc_final: 0.7234 (t0) REVERT: A 2259 MET cc_start: 0.8099 (mmm) cc_final: 0.7690 (mmm) REVERT: A 2428 MET cc_start: 0.8171 (tmm) cc_final: 0.7785 (tmm) REVERT: A 2740 ASP cc_start: 0.8635 (t0) cc_final: 0.8283 (t0) REVERT: A 2829 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 2962 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7472 (ttm-80) REVERT: A 3007 TYR cc_start: 0.7120 (t80) cc_final: 0.6869 (t80) REVERT: A 3310 THR cc_start: 0.3875 (OUTLIER) cc_final: 0.3617 (m) REVERT: A 3320 LEU cc_start: 0.7350 (tt) cc_final: 0.6962 (tp) REVERT: A 3324 CYS cc_start: 0.8722 (m) cc_final: 0.8402 (m) REVERT: A 3401 GLN cc_start: 0.6030 (tp40) cc_final: 0.5630 (tm-30) REVERT: A 3542 GLN cc_start: 0.7677 (mt0) cc_final: 0.7156 (mt0) REVERT: A 3595 MET cc_start: 0.7402 (mmp) cc_final: 0.6763 (tpt) REVERT: A 3714 GLN cc_start: 0.6995 (pp30) cc_final: 0.6755 (pp30) REVERT: A 3767 PHE cc_start: 0.5151 (OUTLIER) cc_final: 0.4352 (t80) REVERT: A 3769 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6681 (m) outliers start: 57 outliers final: 37 residues processed: 296 average time/residue: 0.1598 time to fit residues: 75.6174 Evaluate side-chains 291 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1826 PHE Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2354 SER Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2452 GLU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3310 THR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3644 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 234 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1851 ASN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3714 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 = 0.3804 r_free = 0.3804 target = 0.132900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092256 restraints weight = 39668.994| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.82 r_work: 0.3112 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24398 Z= 0.141 Angle : 0.567 11.709 33015 Z= 0.284 Chirality : 0.041 0.213 3732 Planarity : 0.003 0.047 4157 Dihedral : 6.002 85.303 3208 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.01 % Allowed : 13.62 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2933 helix: 1.85 (0.13), residues: 1540 sheet: -0.75 (0.29), residues: 331 loop : -0.96 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 494 TYR 0.018 0.001 TYR A1420 PHE 0.031 0.001 PHE A1289 TRP 0.028 0.001 TRP A3676 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00331 (24398) covalent geometry : angle 0.56662 (33015) hydrogen bonds : bond 0.03562 ( 1283) hydrogen bonds : angle 4.00767 ( 3747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7193 (t0) cc_final: 0.6880 (t0) REVERT: B 493 MET cc_start: 0.8393 (mtm) cc_final: 0.7949 (mtm) REVERT: B 494 ARG cc_start: 0.7238 (ttp80) cc_final: 0.6704 (tmm-80) REVERT: A 1329 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8302 (tmtt) REVERT: A 1367 ILE cc_start: 0.8446 (mt) cc_final: 0.8156 (mt) REVERT: A 1784 ASP cc_start: 0.8754 (t70) cc_final: 0.8395 (t0) REVERT: A 2171 ASP cc_start: 0.8198 (m-30) cc_final: 0.7822 (m-30) REVERT: A 2247 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7248 (t0) REVERT: A 2259 MET cc_start: 0.8180 (mmm) cc_final: 0.7770 (mmm) REVERT: A 2426 MET cc_start: 0.7912 (tmm) cc_final: 0.7549 (tmm) REVERT: A 2428 MET cc_start: 0.8123 (tmm) cc_final: 0.7721 (tmm) REVERT: A 2439 ASP cc_start: 0.8167 (m-30) cc_final: 0.7778 (m-30) REVERT: A 2740 ASP cc_start: 0.8582 (t0) cc_final: 0.8240 (t0) REVERT: A 2829 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 2962 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7392 (ttm-80) REVERT: A 3007 TYR cc_start: 0.7177 (t80) cc_final: 0.6886 (t80) REVERT: A 3303 LYS cc_start: 0.5859 (mmmt) cc_final: 0.5423 (tppt) REVERT: A 3310 THR cc_start: 0.3895 (OUTLIER) cc_final: 0.3606 (m) REVERT: A 3320 LEU cc_start: 0.7313 (tt) cc_final: 0.6929 (tp) REVERT: A 3324 CYS cc_start: 0.8714 (m) cc_final: 0.8424 (m) REVERT: A 3401 GLN cc_start: 0.6057 (tp40) cc_final: 0.5666 (tm-30) REVERT: A 3595 MET cc_start: 0.7353 (mmp) cc_final: 0.6743 (tpt) REVERT: A 3767 PHE cc_start: 0.5057 (OUTLIER) cc_final: 0.4347 (t80) REVERT: A 3769 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6677 (m) outliers start: 54 outliers final: 37 residues processed: 294 average time/residue: 0.1469 time to fit residues: 69.1159 Evaluate side-chains 292 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2354 SER Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2789 HIS Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3310 THR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 97 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093236 restraints weight = 39540.522| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.81 r_work: 0.3127 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24398 Z= 0.123 Angle : 0.559 12.514 33015 Z= 0.279 Chirality : 0.041 0.214 3732 Planarity : 0.003 0.046 4157 Dihedral : 5.890 84.721 3208 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 1.75 % Allowed : 14.37 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2933 helix: 1.88 (0.13), residues: 1545 sheet: -0.66 (0.29), residues: 329 loop : -0.93 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3543 TYR 0.021 0.001 TYR A2356 PHE 0.031 0.001 PHE A1289 TRP 0.026 0.001 TRP A3676 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00282 (24398) covalent geometry : angle 0.55913 (33015) hydrogen bonds : bond 0.03419 ( 1283) hydrogen bonds : angle 3.94022 ( 3747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7170 (t0) cc_final: 0.6843 (t0) REVERT: B 493 MET cc_start: 0.8368 (mtm) cc_final: 0.7943 (mtm) REVERT: A 1329 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8293 (tmtt) REVERT: A 1367 ILE cc_start: 0.8421 (mt) cc_final: 0.8143 (mt) REVERT: A 2171 ASP cc_start: 0.8210 (m-30) cc_final: 0.7824 (m-30) REVERT: A 2247 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7314 (t0) REVERT: A 2259 MET cc_start: 0.8141 (mmm) cc_final: 0.7720 (mmm) REVERT: A 2356 TYR cc_start: 0.6960 (t80) cc_final: 0.6060 (t80) REVERT: A 2426 MET cc_start: 0.7905 (tmm) cc_final: 0.7539 (tmm) REVERT: A 2428 MET cc_start: 0.8103 (tmm) cc_final: 0.7662 (tmm) REVERT: A 2439 ASP cc_start: 0.8123 (m-30) cc_final: 0.7730 (m-30) REVERT: A 2780 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7899 (ttpt) REVERT: A 2781 ILE cc_start: 0.9279 (mm) cc_final: 0.9017 (tp) REVERT: A 2829 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 2962 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7403 (ttm170) REVERT: A 3007 TYR cc_start: 0.7165 (t80) cc_final: 0.6781 (t80) REVERT: A 3303 LYS cc_start: 0.5787 (mmmt) cc_final: 0.5394 (tppt) REVERT: A 3310 THR cc_start: 0.3889 (OUTLIER) cc_final: 0.3595 (m) REVERT: A 3320 LEU cc_start: 0.7394 (tt) cc_final: 0.7055 (tp) REVERT: A 3324 CYS cc_start: 0.8750 (m) cc_final: 0.8498 (m) REVERT: A 3401 GLN cc_start: 0.6004 (tp40) cc_final: 0.5638 (tm-30) REVERT: A 3518 PHE cc_start: 0.7881 (m-80) cc_final: 0.7423 (m-10) REVERT: A 3528 ARG cc_start: 0.6880 (mmt-90) cc_final: 0.6541 (mmt180) REVERT: A 3555 TYR cc_start: 0.7426 (m-80) cc_final: 0.7088 (m-80) REVERT: A 3595 MET cc_start: 0.7399 (mmp) cc_final: 0.6802 (tpt) REVERT: A 3767 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4470 (t80) REVERT: A 3769 VAL cc_start: 0.6945 (m) cc_final: 0.6672 (m) outliers start: 47 outliers final: 33 residues processed: 290 average time/residue: 0.1527 time to fit residues: 70.5844 Evaluate side-chains 291 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1881 LEU Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2789 HIS Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3310 THR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 253 optimal weight: 0.6980 chunk 195 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.092046 restraints weight = 39904.451| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.82 r_work: 0.3111 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24398 Z= 0.156 Angle : 0.586 12.904 33015 Z= 0.292 Chirality : 0.042 0.164 3732 Planarity : 0.003 0.047 4157 Dihedral : 5.956 86.784 3208 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 14.59 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2933 helix: 1.88 (0.13), residues: 1534 sheet: -0.71 (0.30), residues: 319 loop : -0.97 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 145 TYR 0.018 0.001 TYR A1420 PHE 0.032 0.001 PHE A1289 TRP 0.033 0.001 TRP A3676 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00371 (24398) covalent geometry : angle 0.58591 (33015) hydrogen bonds : bond 0.03545 ( 1283) hydrogen bonds : angle 3.96062 ( 3747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7211 (t0) cc_final: 0.6886 (t0) REVERT: B 493 MET cc_start: 0.8352 (mtm) cc_final: 0.7982 (mtm) REVERT: A 1329 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8287 (tmtt) REVERT: A 1367 ILE cc_start: 0.8428 (mt) cc_final: 0.8151 (mt) REVERT: A 1784 ASP cc_start: 0.8748 (t70) cc_final: 0.8395 (t0) REVERT: A 2171 ASP cc_start: 0.8229 (m-30) cc_final: 0.7898 (m-30) REVERT: A 2247 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7166 (t70) REVERT: A 2356 TYR cc_start: 0.6895 (t80) cc_final: 0.6009 (t80) REVERT: A 2426 MET cc_start: 0.7919 (tmm) cc_final: 0.7544 (tmm) REVERT: A 2428 MET cc_start: 0.8111 (tmm) cc_final: 0.7704 (tmm) REVERT: A 2439 ASP cc_start: 0.8166 (m-30) cc_final: 0.7780 (m-30) REVERT: A 2780 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7931 (ttpt) REVERT: A 2829 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 2962 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7413 (ttm170) REVERT: A 3007 TYR cc_start: 0.7304 (t80) cc_final: 0.6953 (t80) REVERT: A 3303 LYS cc_start: 0.5837 (mmmt) cc_final: 0.5424 (tptt) REVERT: A 3310 THR cc_start: 0.3804 (OUTLIER) cc_final: 0.3514 (m) REVERT: A 3320 LEU cc_start: 0.7318 (tt) cc_final: 0.6960 (tp) REVERT: A 3324 CYS cc_start: 0.8725 (m) cc_final: 0.8464 (m) REVERT: A 3401 GLN cc_start: 0.6011 (tp40) cc_final: 0.5656 (tm-30) REVERT: A 3438 LYS cc_start: 0.7685 (tptp) cc_final: 0.7222 (mmmm) REVERT: A 3555 TYR cc_start: 0.7410 (m-80) cc_final: 0.7122 (m-80) REVERT: A 3595 MET cc_start: 0.7393 (mmp) cc_final: 0.6814 (tpt) REVERT: A 3767 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4321 (t80) REVERT: A 3769 VAL cc_start: 0.6944 (m) cc_final: 0.6700 (m) outliers start: 45 outliers final: 38 residues processed: 285 average time/residue: 0.1685 time to fit residues: 77.3874 Evaluate side-chains 294 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1881 LEU Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2789 HIS Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3310 THR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3415 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3884 LEU Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 108 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 GLN A3741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092221 restraints weight = 39874.169| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.81 r_work: 0.3113 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24398 Z= 0.150 Angle : 0.582 13.047 33015 Z= 0.290 Chirality : 0.042 0.167 3732 Planarity : 0.003 0.048 4157 Dihedral : 5.968 88.778 3208 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 1.71 % Allowed : 14.70 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2933 helix: 1.88 (0.13), residues: 1538 sheet: -0.66 (0.29), residues: 330 loop : -0.98 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 145 TYR 0.020 0.001 TYR A1420 PHE 0.031 0.001 PHE A1289 TRP 0.042 0.001 TRP A3676 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00355 (24398) covalent geometry : angle 0.58237 (33015) hydrogen bonds : bond 0.03514 ( 1283) hydrogen bonds : angle 3.95075 ( 3747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: B 183 ASP cc_start: 0.7206 (t0) cc_final: 0.6887 (t0) REVERT: B 493 MET cc_start: 0.8308 (mtm) cc_final: 0.7910 (mtm) REVERT: B 494 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6928 (ttp80) REVERT: A 1329 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8294 (tmtt) REVERT: A 1367 ILE cc_start: 0.8413 (mt) cc_final: 0.8137 (mt) REVERT: A 1784 ASP cc_start: 0.8741 (t70) cc_final: 0.8392 (t0) REVERT: A 2171 ASP cc_start: 0.8227 (m-30) cc_final: 0.7896 (m-30) REVERT: A 2247 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7081 (t0) REVERT: A 2356 TYR cc_start: 0.6935 (t80) cc_final: 0.6020 (t80) REVERT: A 2426 MET cc_start: 0.7958 (tmm) cc_final: 0.7584 (tmm) REVERT: A 2428 MET cc_start: 0.8104 (tmm) cc_final: 0.7696 (tmm) REVERT: A 2439 ASP cc_start: 0.8171 (m-30) cc_final: 0.7782 (m-30) REVERT: A 2829 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 2962 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7428 (ttm170) REVERT: A 3007 TYR cc_start: 0.7157 (t80) cc_final: 0.6882 (t80) REVERT: A 3303 LYS cc_start: 0.5594 (mmmt) cc_final: 0.5279 (tptt) REVERT: A 3310 THR cc_start: 0.3768 (OUTLIER) cc_final: 0.3428 (m) REVERT: A 3320 LEU cc_start: 0.7392 (tt) cc_final: 0.7065 (tp) REVERT: A 3324 CYS cc_start: 0.8750 (m) cc_final: 0.8498 (m) REVERT: A 3401 GLN cc_start: 0.6135 (tp40) cc_final: 0.5629 (tm-30) REVERT: A 3438 LYS cc_start: 0.7684 (tptp) cc_final: 0.7295 (mmmm) REVERT: A 3528 ARG cc_start: 0.6881 (mmt-90) cc_final: 0.6642 (mmt180) REVERT: A 3555 TYR cc_start: 0.7477 (m-80) cc_final: 0.7202 (m-80) REVERT: A 3595 MET cc_start: 0.7367 (mmp) cc_final: 0.6815 (tpt) REVERT: A 3767 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.4327 (t80) REVERT: A 3769 VAL cc_start: 0.6946 (OUTLIER) cc_final: 0.6699 (m) outliers start: 46 outliers final: 38 residues processed: 289 average time/residue: 0.1659 time to fit residues: 77.1304 Evaluate side-chains 295 residues out of total 2687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1507 THR Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1720 THR Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1881 LEU Chi-restraints excluded: chain A residue 2081 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2380 LEU Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain A residue 2472 THR Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2671 GLN Chi-restraints excluded: chain A residue 2789 HIS Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2843 LEU Chi-restraints excluded: chain A residue 3310 THR Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3358 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3407 LEU Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3714 GLN Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3767 PHE Chi-restraints excluded: chain A residue 3769 VAL Chi-restraints excluded: chain A residue 3856 HIS Chi-restraints excluded: chain A residue 3980 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092186 restraints weight = 39704.758| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.82 r_work: 0.3103 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 24398 Z= 0.167 Angle : 0.729 58.878 33015 Z= 0.395 Chirality : 0.044 0.836 3732 Planarity : 0.003 0.048 4157 Dihedral : 5.968 88.760 3208 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 1.67 % Allowed : 14.85 % Favored : 83.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2933 helix: 1.88 (0.13), residues: 1538 sheet: -0.66 (0.29), residues: 330 loop : -0.98 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.016 0.001 TYR A1420 PHE 0.021 0.001 PHE A1826 TRP 0.037 0.001 TRP A3676 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00386 (24398) covalent geometry : angle 0.72907 (33015) hydrogen bonds : bond 0.03509 ( 1283) hydrogen bonds : angle 3.95170 ( 3747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5229.43 seconds wall clock time: 90 minutes 53.30 seconds (5453.30 seconds total)