Starting phenix.real_space_refine on Mon Jun 16 15:12:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.map" model { file = "/net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9djy_46940/06_2025/9djy_46940.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.039 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 9 5.49 5 Mg 1 5.21 5 S 79 5.16 5 C 11795 2.51 5 N 3094 2.21 5 O 3446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2341, 18311 Classifications: {'peptide': 2341} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 65, 'TRANS': 2275} Unresolved chain links: 1 Chain breaks: 11 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 768 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 8, 'GLU:plan': 32, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 349 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 11.44, per 1000 atoms: 0.62 Number of scatterers: 18424 At special positions: 0 Unit cell: (102.08, 141.52, 163.56, 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 79 16.00 P 9 15.00 Mg 1 11.99 O 3446 8.00 N 3094 7.00 C 11795 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: 4.80 Conformation dependent library (CDL) restraints added in 2.9 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 63.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 1433 through 1461 Processing helix chain 'A' and resid 1471 through 1494 Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 4.004A pdb=" N SER A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 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 1557 through 1566 removed outlier: 3.932A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 4.181A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.853A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.598A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1687 Processing helix chain 'A' and resid 1688 through 1690 No H-bonds generated for 'chain 'A' and resid 1688 through 1690' Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.815A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.177A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.735A pdb=" N GLN A1840 " --> pdb=" O VAL A1836 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A1841 " --> pdb=" O GLY A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.682A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1850 through 1853' Processing helix chain 'A' and resid 1854 through 1874 removed outlier: 3.657A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.546A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.693A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2003 Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2008 through 2022 removed outlier: 3.699A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2065 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 2140 removed outlier: 3.539A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2204 through 2209 removed outlier: 3.928A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2237 Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.522A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.880A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2299 removed outlier: 3.649A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 4.086A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.772A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.664A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2581 through 2587 removed outlier: 6.489A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.982A 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 2657 through 2660 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2709 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.685A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.805A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.695A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2864 Processing helix chain 'A' and resid 2869 through 2884 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 2934 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.690A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3299 Processing helix chain 'A' and resid 3299 through 3318 removed outlier: 4.388A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 removed outlier: 3.666A pdb=" N PHE A3334 " --> pdb=" O TYR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3372 through 3383 removed outlier: 3.505A pdb=" N GLY A3383 " --> pdb=" O TRP A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.622A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3512 removed outlier: 3.772A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.613A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3741 through 3753 Processing helix chain 'A' and resid 3755 through 3768 removed outlier: 4.050A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3836 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 3861 removed outlier: 3.685A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.514A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3914 removed outlier: 3.718A pdb=" N GLN A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3945 through 3950 removed outlier: 3.959A pdb=" N PHE A3950 " --> pdb=" O VAL A3946 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.958A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.940A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.547A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 removed outlier: 3.612A pdb=" N PHE A1748 " --> pdb=" O TYR A1735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1821 removed outlier: 6.520A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2099 through 2104 removed outlier: 6.223A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2118 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.027A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 removed outlier: 3.744A pdb=" N PHE A2515 " --> pdb=" O VAL A2524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.692A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.862A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.299A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.788A pdb=" N ARG A3476 " --> pdb=" O ALA A3473 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3813 through 3815 1107 hydrogen bonds defined for protein. 3276 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: 9.98 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5930 1.35 - 1.46: 4386 1.46 - 1.58: 8339 1.58 - 1.70: 11 1.70 - 1.82: 126 Bond restraints: 18792 Sorted by residual: bond pdb=" C LEU A2491 " pdb=" N PRO A2492 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.41e+00 bond pdb=" CB MET A3414 " pdb=" CG MET A3414 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.51e+00 bond pdb=" C PHE A3608 " pdb=" N PRO A3609 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.30e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 18787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 25160 2.19 - 4.37: 273 4.37 - 6.56: 39 6.56 - 8.75: 5 8.75 - 10.94: 3 Bond angle restraints: 25480 Sorted by residual: angle pdb=" CB MET A3414 " pdb=" CG MET A3414 " pdb=" SD MET A3414 " ideal model delta sigma weight residual 112.70 101.76 10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA LYS A2979 " pdb=" CB LYS A2979 " pdb=" CG LYS A2979 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CB MET A2980 " pdb=" CG MET A2980 " pdb=" SD MET A2980 " ideal model delta sigma weight residual 112.70 121.68 -8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 119.00 -5.40 1.90e+00 2.77e-01 8.06e+00 angle pdb=" CB MET A1655 " pdb=" CG MET A1655 " pdb=" SD MET A1655 " ideal model delta sigma weight residual 112.70 120.86 -8.16 3.00e+00 1.11e-01 7.41e+00 ... (remaining 25475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 10920 31.92 - 63.84: 306 63.84 - 95.76: 26 95.76 - 127.68: 0 127.68 - 159.60: 1 Dihedral angle restraints: 11253 sinusoidal: 4396 harmonic: 6857 Sorted by residual: dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -108.86 -159.60 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" CA GLN A1603 " pdb=" C GLN A1603 " pdb=" N ALA A1604 " pdb=" CA ALA A1604 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLU A3319 " pdb=" C GLU A3319 " pdb=" N LEU A3320 " pdb=" CA LEU A3320 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2559 0.062 - 0.123: 357 0.123 - 0.185: 18 0.185 - 0.247: 2 0.247 - 0.308: 1 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CB ILE A2222 " pdb=" CA ILE A2222 " pdb=" CG1 ILE A2222 " pdb=" CG2 ILE A2222 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE A3415 " pdb=" CA ILE A3415 " pdb=" CG1 ILE A3415 " pdb=" CG2 ILE A3415 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A1861 " pdb=" CA VAL A1861 " pdb=" CG1 VAL A1861 " pdb=" CG2 VAL A1861 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2934 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A2619 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3653 " 0.017 2.00e-02 2.50e+03 1.43e-02 3.60e+00 pdb=" CG PHE A3653 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A3653 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A3653 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A3653 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A3653 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A3653 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A4024 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A4025 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A4025 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A4025 " -0.024 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 142 2.60 - 3.18: 15341 3.18 - 3.75: 29166 3.75 - 4.33: 37567 4.33 - 4.90: 63673 Nonbonded interactions: 145889 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.031 2.170 nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.133 2.170 nonbonded pdb=" NH2 ARG A3342 " pdb=" OD1 ASN A3393 " model vdw 2.254 3.120 nonbonded pdb=" O PRO A2419 " pdb=" OG SER A2422 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A3943 " pdb=" O TYR A3954 " model vdw 2.271 3.040 ... (remaining 145884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 48.370 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.003 0.043 18792 Z= 0.140 Angle : 0.586 10.935 25480 Z= 0.299 Chirality : 0.042 0.308 2937 Planarity : 0.004 0.054 3204 Dihedral : 14.619 159.597 6797 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2315 helix: 1.17 (0.13), residues: 1389 sheet: 0.09 (0.39), residues: 196 loop : -1.02 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A3748 HIS 0.014 0.001 HIS A3413 PHE 0.033 0.001 PHE A3653 TYR 0.016 0.001 TYR A2571 ARG 0.003 0.000 ARG A2771 Details of bonding type rmsd hydrogen bonds : bond 0.12431 ( 1107) hydrogen bonds : angle 5.17447 ( 3276) covalent geometry : bond 0.00315 (18792) covalent geometry : angle 0.58567 (25480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.927 Fit side-chains REVERT: A 2017 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7177 (mm-30) REVERT: A 2155 ASP cc_start: 0.8277 (t0) cc_final: 0.7871 (t0) REVERT: A 2689 ILE cc_start: 0.8908 (pt) cc_final: 0.8452 (mt) REVERT: A 2881 ILE cc_start: 0.9105 (tt) cc_final: 0.8904 (tt) REVERT: A 3344 ASP cc_start: 0.7599 (t70) cc_final: 0.7339 (t0) REVERT: A 3345 MET cc_start: 0.7563 (mmm) cc_final: 0.6916 (mmm) REVERT: A 3377 MET cc_start: 0.7938 (tpp) cc_final: 0.7551 (mmt) REVERT: A 3720 LEU cc_start: 0.7768 (mm) cc_final: 0.7538 (mm) REVERT: A 3793 ASP cc_start: 0.7248 (t70) cc_final: 0.6537 (t0) REVERT: A 4087 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6667 (mm-40) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2653 time to fit residues: 97.1422 Evaluate side-chains 149 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1840 GLN A1851 ASN A1891 HIS A2198 ASN ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4022 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096045 restraints weight = 36644.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099024 restraints weight = 18735.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100966 restraints weight = 12206.624| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18792 Z= 0.181 Angle : 0.539 7.322 25480 Z= 0.277 Chirality : 0.041 0.179 2937 Planarity : 0.004 0.046 3204 Dihedral : 6.218 157.665 2561 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.66 % Allowed : 9.50 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2315 helix: 1.95 (0.14), residues: 1382 sheet: -0.23 (0.36), residues: 223 loop : -0.83 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.007 0.001 HIS A3413 PHE 0.024 0.001 PHE A2585 TYR 0.015 0.001 TYR A2571 ARG 0.010 0.000 ARG A2460 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1107) hydrogen bonds : angle 4.03720 ( 3276) covalent geometry : bond 0.00425 (18792) covalent geometry : angle 0.53905 (25480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 2.182 Fit side-chains REVERT: A 2107 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8799 (mmtm) REVERT: A 2155 ASP cc_start: 0.8345 (t0) cc_final: 0.8094 (t0) REVERT: A 2487 ASP cc_start: 0.7907 (t0) cc_final: 0.7696 (t0) REVERT: A 2689 ILE cc_start: 0.8929 (pt) cc_final: 0.8500 (mt) REVERT: A 2770 THR cc_start: 0.9251 (m) cc_final: 0.8916 (p) REVERT: A 2796 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7969 (t0) REVERT: A 3344 ASP cc_start: 0.7677 (t70) cc_final: 0.7424 (t0) REVERT: A 3345 MET cc_start: 0.7528 (mmm) cc_final: 0.7054 (mmm) REVERT: A 3377 MET cc_start: 0.7967 (tpp) cc_final: 0.7615 (mmt) REVERT: A 3638 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 4087 GLN cc_start: 0.7456 (tm-30) cc_final: 0.6788 (mm-40) outliers start: 13 outliers final: 7 residues processed: 175 average time/residue: 0.2678 time to fit residues: 78.2109 Evaluate side-chains 156 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2796 ASP Chi-restraints excluded: chain A residue 3325 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3638 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1788 GLN A2198 ASN ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2753 GLN ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4022 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097944 restraints weight = 36430.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100929 restraints weight = 18570.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102899 restraints weight = 12057.006| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18792 Z= 0.122 Angle : 0.484 7.720 25480 Z= 0.246 Chirality : 0.039 0.154 2937 Planarity : 0.003 0.045 3204 Dihedral : 6.092 156.627 2561 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.07 % Allowed : 11.19 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2315 helix: 2.20 (0.14), residues: 1387 sheet: -0.16 (0.36), residues: 224 loop : -0.74 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS A3413 PHE 0.017 0.001 PHE A2585 TYR 0.015 0.001 TYR A2630 ARG 0.005 0.000 ARG A2460 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 1107) hydrogen bonds : angle 3.79828 ( 3276) covalent geometry : bond 0.00279 (18792) covalent geometry : angle 0.48423 (25480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 2.278 Fit side-chains REVERT: A 1560 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8169 (mppt) REVERT: A 2107 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8754 (mmtm) REVERT: A 2155 ASP cc_start: 0.8323 (t0) cc_final: 0.8122 (t0) REVERT: A 2487 ASP cc_start: 0.7894 (t0) cc_final: 0.7608 (t0) REVERT: A 2689 ILE cc_start: 0.8861 (pt) cc_final: 0.8482 (mt) REVERT: A 2796 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (t0) REVERT: A 3344 ASP cc_start: 0.7695 (t70) cc_final: 0.7390 (t0) REVERT: A 3377 MET cc_start: 0.7948 (tpp) cc_final: 0.7597 (mmt) REVERT: A 3638 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 4087 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7097 (mm-40) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 0.2582 time to fit residues: 79.9186 Evaluate side-chains 169 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2344 THR Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2796 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3638 PHE Chi-restraints excluded: chain A residue 3653 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 168 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2198 ASN ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4022 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094500 restraints weight = 36278.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097552 restraints weight = 18454.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099557 restraints weight = 12001.722| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18792 Z= 0.136 Angle : 0.491 6.495 25480 Z= 0.250 Chirality : 0.039 0.144 2937 Planarity : 0.003 0.043 3204 Dihedral : 6.078 156.103 2561 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.79 % Allowed : 12.57 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2315 helix: 2.35 (0.14), residues: 1388 sheet: -0.04 (0.37), residues: 207 loop : -0.73 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.006 0.001 HIS A3413 PHE 0.017 0.001 PHE A3313 TYR 0.014 0.001 TYR A3364 ARG 0.004 0.000 ARG A2460 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1107) hydrogen bonds : angle 3.69457 ( 3276) covalent geometry : bond 0.00319 (18792) covalent geometry : angle 0.49150 (25480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: A 2107 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8785 (mmtt) REVERT: A 2155 ASP cc_start: 0.8346 (t0) cc_final: 0.8130 (t0) REVERT: A 2689 ILE cc_start: 0.8868 (pt) cc_final: 0.8482 (mt) REVERT: A 2753 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: A 2770 THR cc_start: 0.9199 (m) cc_final: 0.8897 (p) REVERT: A 2940 PHE cc_start: 0.7550 (p90) cc_final: 0.7308 (p90) REVERT: A 3330 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8169 (t80) REVERT: A 3344 ASP cc_start: 0.7714 (t70) cc_final: 0.7469 (t0) REVERT: A 3345 MET cc_start: 0.7477 (mmm) cc_final: 0.6675 (mmm) REVERT: A 3793 ASP cc_start: 0.7219 (t0) cc_final: 0.6670 (t0) REVERT: A 4087 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7111 (mm-40) outliers start: 35 outliers final: 20 residues processed: 196 average time/residue: 0.2741 time to fit residues: 90.2770 Evaluate side-chains 182 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2344 THR Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3913 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 2 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 179 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2198 ASN ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4077 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096922 restraints weight = 36795.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099933 restraints weight = 18763.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101941 restraints weight = 12202.539| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18792 Z= 0.118 Angle : 0.485 9.718 25480 Z= 0.244 Chirality : 0.039 0.158 2937 Planarity : 0.003 0.043 3204 Dihedral : 6.007 155.619 2561 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.38 % Allowed : 14.10 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.18), residues: 2315 helix: 2.42 (0.14), residues: 1390 sheet: -0.08 (0.37), residues: 216 loop : -0.62 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS A3413 PHE 0.015 0.001 PHE A3708 TYR 0.013 0.001 TYR A2571 ARG 0.004 0.000 ARG A2460 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1107) hydrogen bonds : angle 3.61591 ( 3276) covalent geometry : bond 0.00273 (18792) covalent geometry : angle 0.48524 (25480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 2107 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8703 (mmtm) REVERT: A 2487 ASP cc_start: 0.8051 (t0) cc_final: 0.7678 (t0) REVERT: A 2689 ILE cc_start: 0.8785 (pt) cc_final: 0.8472 (mt) REVERT: A 2753 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: A 2770 THR cc_start: 0.9201 (m) cc_final: 0.8929 (p) REVERT: A 2940 PHE cc_start: 0.7428 (p90) cc_final: 0.7225 (p90) REVERT: A 3330 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8198 (t80) REVERT: A 3344 ASP cc_start: 0.7601 (t70) cc_final: 0.7316 (t0) REVERT: A 4087 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7134 (mm-40) outliers start: 27 outliers final: 18 residues processed: 189 average time/residue: 0.2548 time to fit residues: 81.2884 Evaluate side-chains 178 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3913 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 178 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 174 optimal weight: 0.0870 chunk 151 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2198 ASN ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** 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 = 0.3697 r_free = 0.3697 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095404 restraints weight = 36203.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098464 restraints weight = 18393.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100486 restraints weight = 11964.710| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18792 Z= 0.111 Angle : 0.478 8.368 25480 Z= 0.240 Chirality : 0.038 0.151 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.950 155.388 2561 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.48 % Allowed : 14.72 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2315 helix: 2.45 (0.14), residues: 1395 sheet: -0.04 (0.38), residues: 206 loop : -0.62 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.006 0.001 HIS A3413 PHE 0.011 0.001 PHE A3313 TYR 0.013 0.001 TYR A2571 ARG 0.003 0.000 ARG A2460 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1107) hydrogen bonds : angle 3.57283 ( 3276) covalent geometry : bond 0.00254 (18792) covalent geometry : angle 0.47834 (25480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 2107 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8687 (mmtm) REVERT: A 2410 SER cc_start: 0.9072 (t) cc_final: 0.8796 (p) REVERT: A 2428 MET cc_start: 0.8056 (ttm) cc_final: 0.7842 (tmm) REVERT: A 2689 ILE cc_start: 0.8784 (pt) cc_final: 0.8482 (mt) REVERT: A 2753 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: A 2770 THR cc_start: 0.9184 (m) cc_final: 0.8892 (p) REVERT: A 2797 MET cc_start: 0.7633 (mmm) cc_final: 0.7409 (mmt) REVERT: A 2940 PHE cc_start: 0.7387 (p90) cc_final: 0.7147 (p90) REVERT: A 3330 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8213 (t80) REVERT: A 3344 ASP cc_start: 0.7697 (t70) cc_final: 0.7470 (t0) REVERT: A 3793 ASP cc_start: 0.7134 (t0) cc_final: 0.6661 (t0) REVERT: A 4087 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7137 (mm-40) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.2598 time to fit residues: 84.1406 Evaluate side-chains 186 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3430 SER Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3913 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 130 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 228 optimal weight: 0.0670 chunk 204 optimal weight: 0.1980 chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098499 restraints weight = 36332.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101560 restraints weight = 18537.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103581 restraints weight = 12023.913| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18792 Z= 0.096 Angle : 0.472 9.232 25480 Z= 0.236 Chirality : 0.038 0.153 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.856 155.234 2561 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.33 % Allowed : 15.33 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.18), residues: 2315 helix: 2.53 (0.14), residues: 1397 sheet: 0.08 (0.38), residues: 206 loop : -0.60 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.005 0.000 HIS A3413 PHE 0.012 0.001 PHE A3406 TYR 0.011 0.001 TYR A2571 ARG 0.004 0.000 ARG A3340 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 1107) hydrogen bonds : angle 3.50407 ( 3276) covalent geometry : bond 0.00211 (18792) covalent geometry : angle 0.47188 (25480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 2021 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 2107 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8667 (mmtt) REVERT: A 2410 SER cc_start: 0.8992 (t) cc_final: 0.8727 (p) REVERT: A 2689 ILE cc_start: 0.8759 (pt) cc_final: 0.8463 (mt) REVERT: A 2753 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: A 2940 PHE cc_start: 0.7361 (p90) cc_final: 0.7091 (p90) REVERT: A 3330 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 3344 ASP cc_start: 0.7703 (t70) cc_final: 0.7416 (t0) REVERT: A 3399 ASN cc_start: 0.8785 (t0) cc_final: 0.7805 (t0) REVERT: A 4087 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7117 (mm-40) outliers start: 26 outliers final: 18 residues processed: 189 average time/residue: 0.2536 time to fit residues: 80.1264 Evaluate side-chains 177 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3913 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2837 ASN ** A3975 ASN ** 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 = 0.3723 r_free = 0.3723 target = 0.123999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098729 restraints weight = 36465.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101758 restraints weight = 18588.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103740 restraints weight = 12060.307| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18792 Z= 0.100 Angle : 0.477 8.551 25480 Z= 0.239 Chirality : 0.038 0.161 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.833 154.984 2561 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.53 % Allowed : 15.53 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.18), residues: 2315 helix: 2.54 (0.14), residues: 1398 sheet: 0.13 (0.38), residues: 206 loop : -0.58 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.005 0.000 HIS A3413 PHE 0.013 0.001 PHE A2943 TYR 0.020 0.001 TYR A3927 ARG 0.004 0.000 ARG A3340 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 1107) hydrogen bonds : angle 3.48819 ( 3276) covalent geometry : bond 0.00223 (18792) covalent geometry : angle 0.47694 (25480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 2021 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8092 (tp) REVERT: A 2107 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8648 (mmtt) REVERT: A 2410 SER cc_start: 0.9077 (t) cc_final: 0.8778 (p) REVERT: A 2625 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8504 (tp) REVERT: A 2689 ILE cc_start: 0.8713 (pt) cc_final: 0.8417 (mt) REVERT: A 2753 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: A 2940 PHE cc_start: 0.7354 (p90) cc_final: 0.7067 (p90) REVERT: A 3330 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8159 (t80) REVERT: A 3344 ASP cc_start: 0.7738 (t70) cc_final: 0.7421 (t0) REVERT: A 3399 ASN cc_start: 0.8778 (t0) cc_final: 0.7820 (t0) REVERT: A 4052 THR cc_start: 0.9299 (m) cc_final: 0.8919 (p) REVERT: A 4087 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7105 (mm-40) outliers start: 30 outliers final: 24 residues processed: 186 average time/residue: 0.2596 time to fit residues: 81.1801 Evaluate side-chains 189 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2794 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3913 SER Chi-restraints excluded: chain A residue 4024 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 92 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097257 restraints weight = 36946.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100241 restraints weight = 18774.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102193 restraints weight = 12187.443| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18792 Z= 0.128 Angle : 0.498 8.246 25480 Z= 0.250 Chirality : 0.039 0.163 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.876 154.343 2561 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.53 % Allowed : 15.99 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2315 helix: 2.51 (0.14), residues: 1398 sheet: 0.09 (0.38), residues: 205 loop : -0.59 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.005 0.001 HIS A3413 PHE 0.035 0.001 PHE A1708 TYR 0.023 0.001 TYR A3927 ARG 0.003 0.000 ARG A3340 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 1107) hydrogen bonds : angle 3.51159 ( 3276) covalent geometry : bond 0.00300 (18792) covalent geometry : angle 0.49840 (25480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 2.231 Fit side-chains revert: symmetry clash REVERT: A 2021 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 2107 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8661 (mmmt) REVERT: A 2410 SER cc_start: 0.9038 (t) cc_final: 0.8755 (p) REVERT: A 2689 ILE cc_start: 0.8727 (pt) cc_final: 0.8360 (mt) REVERT: A 2753 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: A 2770 THR cc_start: 0.9220 (m) cc_final: 0.8895 (p) REVERT: A 2940 PHE cc_start: 0.7341 (p90) cc_final: 0.7034 (p90) REVERT: A 3330 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 3344 ASP cc_start: 0.7777 (t70) cc_final: 0.7470 (t0) REVERT: A 3399 ASN cc_start: 0.8740 (t0) cc_final: 0.7747 (t0) REVERT: A 4052 THR cc_start: 0.9290 (m) cc_final: 0.8926 (p) REVERT: A 4087 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7127 (mm-40) outliers start: 30 outliers final: 23 residues processed: 182 average time/residue: 0.2589 time to fit residues: 79.8262 Evaluate side-chains 187 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2756 MET Chi-restraints excluded: chain A residue 2794 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3913 SER Chi-restraints excluded: chain A residue 4024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 152 optimal weight: 0.0010 chunk 96 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.124007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098721 restraints weight = 36623.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101755 restraints weight = 18589.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103748 restraints weight = 12073.917| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18792 Z= 0.099 Angle : 0.489 6.864 25480 Z= 0.245 Chirality : 0.038 0.169 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.817 154.037 2561 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.53 % Allowed : 16.04 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.18), residues: 2315 helix: 2.56 (0.14), residues: 1399 sheet: 0.21 (0.38), residues: 206 loop : -0.57 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.005 0.000 HIS A3413 PHE 0.032 0.001 PHE A1708 TYR 0.024 0.001 TYR A3927 ARG 0.003 0.000 ARG A3340 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1107) hydrogen bonds : angle 3.49835 ( 3276) covalent geometry : bond 0.00220 (18792) covalent geometry : angle 0.48920 (25480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: A 2021 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 2107 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8653 (mmtt) REVERT: A 2410 SER cc_start: 0.8985 (t) cc_final: 0.8749 (p) REVERT: A 2625 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8492 (tp) REVERT: A 2689 ILE cc_start: 0.8716 (pt) cc_final: 0.8348 (mt) REVERT: A 2753 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 2940 PHE cc_start: 0.7384 (p90) cc_final: 0.7094 (p90) REVERT: A 3330 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8190 (t80) REVERT: A 3344 ASP cc_start: 0.7716 (t70) cc_final: 0.7375 (t0) REVERT: A 3399 ASN cc_start: 0.8800 (t0) cc_final: 0.7809 (t0) REVERT: A 3722 MET cc_start: 0.8916 (mmt) cc_final: 0.8668 (mmp) REVERT: A 4052 THR cc_start: 0.9277 (m) cc_final: 0.8915 (p) REVERT: A 4087 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7116 (mm-40) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.2512 time to fit residues: 78.6479 Evaluate side-chains 185 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2794 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3370 LEU Chi-restraints excluded: chain A residue 3387 ASN Chi-restraints excluded: chain A residue 3547 ASP Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3653 PHE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3913 SER Chi-restraints excluded: chain A residue 4024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 85 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 181 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097954 restraints weight = 36569.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100980 restraints weight = 18681.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102985 restraints weight = 12166.992| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18792 Z= 0.111 Angle : 0.490 6.739 25480 Z= 0.246 Chirality : 0.038 0.170 2937 Planarity : 0.003 0.043 3204 Dihedral : 5.828 153.628 2561 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.53 % Allowed : 16.20 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.18), residues: 2315 helix: 2.59 (0.14), residues: 1399 sheet: 0.21 (0.38), residues: 206 loop : -0.56 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.005 0.001 HIS A3413 PHE 0.030 0.001 PHE A1708 TYR 0.024 0.001 TYR A3927 ARG 0.003 0.000 ARG A3894 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 1107) hydrogen bonds : angle 3.49234 ( 3276) covalent geometry : bond 0.00255 (18792) covalent geometry : angle 0.48961 (25480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5704.81 seconds wall clock time: 100 minutes 3.55 seconds (6003.55 seconds total)