Starting phenix.real_space_refine on Fri Sep 19 00:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dk0_46942/09_2025/9dk0_46942.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 94 5.16 5 C 13479 2.51 5 N 3560 2.21 5 O 3907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21050 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2344, 18250 Classifications: {'peptide': 2344} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 65, 'TRANS': 2278} Chain breaks: 10 Unresolved non-hydrogen bonds: 702 Unresolved non-hydrogen angles: 872 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 39, 'GLN:plan1': 7, 'ASN:plan1': 12, 'TRP:plan': 1, 'PHE:plan': 8, 'TYR:plan': 3, 'ASP:plan': 23, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 402 Chain: "C" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2687 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 5, 'TRP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 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: 4.86, per 1000 atoms: 0.23 Number of scatterers: 21050 At special positions: 0 Unit cell: (100.92, 142.68, 169.36, 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 94 16.00 P 9 15.00 Mg 1 11.99 O 3907 8.00 N 3560 7.00 C 13479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 921.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 23 sheets defined 56.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 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 1520 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 1550 Processing helix chain 'A' and resid 1558 through 1560 No H-bonds generated for 'chain 'A' and resid 1558 through 1560' Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.752A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.820A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 3.976A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.855A pdb=" N ALA A1724 " --> pdb=" O THR A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1787 Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.611A pdb=" N GLN A1840 " --> pdb=" O VAL A1836 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A1841 " --> pdb=" O GLY A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.653A 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 1875 removed outlier: 3.775A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.460A 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: 3.730A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1959 Processing helix chain 'A' and resid 1969 through 1988 removed outlier: 4.043A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 5.117A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.622A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) 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: 3.900A 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 Processing helix chain 'A' and resid 2144 through 2146 No H-bonds generated for 'chain 'A' and resid 2144 through 2146' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.567A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2208 removed outlier: 3.545A pdb=" N ILE A2207 " --> pdb=" O THR A2203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A2208 " --> pdb=" O PRO A2204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2203 through 2208' Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.596A pdb=" N LEU A2237 " --> pdb=" O SER A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2258 through 2269 Processing helix chain 'A' and resid 2270 through 2272 No H-bonds generated for 'chain 'A' and resid 2270 through 2272' Processing helix chain 'A' and resid 2283 through 2299 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 2382 through 2387 removed outlier: 3.908A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.938A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.668A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.952A 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 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.201A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.822A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A2593 " --> pdb=" O THR A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.922A 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 2662 through 2681 Processing helix chain 'A' and resid 2690 through 2694 removed outlier: 3.916A pdb=" N LEU A2694 " --> pdb=" O SER A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.753A pdb=" N LEU A2712 " --> pdb=" O ASN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.750A 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: 3.840A 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: 3.874A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 removed outlier: 3.819A pdb=" N LEU A2843 " --> pdb=" O ILE A2840 " (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 2904 Processing helix chain 'A' and resid 2905 through 2912 removed outlier: 3.532A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.885A 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 3298 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.430A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 removed outlier: 3.574A pdb=" N PHE A3334 " --> pdb=" O TYR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.601A pdb=" N PHE A3356 " --> pdb=" O LEU A3352 " (cutoff:3.500A) Processing helix chain 'A' and resid 3365 through 3370 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.369A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3513 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3571 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.631A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.952A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) 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 removed outlier: 3.833A pdb=" N ARG A3745 " --> pdb=" O ASN A3741 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.507A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.948A 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 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 4.150A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.575A pdb=" N LEU A3889 " --> pdb=" O PRO A3885 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3914 Processing helix chain 'A' and resid 3923 through 3945 removed outlier: 3.862A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A3945 " --> pdb=" O ALA A3941 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.800A 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 4001 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 4.128A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.013A pdb=" N SER C 405 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.519A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A1596 " --> pdb=" O ILE A1579 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 removed outlier: 3.624A pdb=" N PHE A1748 " --> pdb=" O TYR A1735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.825A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.628A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 removed outlier: 3.512A pdb=" N ARG A2126 " --> pdb=" O SER A2117 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A2124 " --> pdb=" O LEU A2119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.525A pdb=" N VAL A2360 " --> pdb=" O SER A2367 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A2367 " --> pdb=" O VAL A2360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.044A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2464 Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.588A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.366A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.032A 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: 4.745A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3813 through 3815 Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.863A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.166A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 480 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.810A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 222 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 233 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 247 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 263 removed outlier: 7.341A pdb=" N VAL C 279 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR C 292 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.902A pdb=" N ASP C 304 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 310 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 319 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL C 332 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 340 through 345 removed outlier: 3.630A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 420 through 426 removed outlier: 4.183A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6721 1.34 - 1.46: 3811 1.46 - 1.58: 10800 1.58 - 1.70: 13 1.70 - 1.82: 146 Bond restraints: 21491 Sorted by residual: bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.88e+00 bond pdb=" CB GLU C 386 " pdb=" CG GLU C 386 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB GLN A1665 " pdb=" CG GLN A1665 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" C4 ADP A4103 " pdb=" C5 ADP A4103 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" CB ASP A2818 " pdb=" CG ASP A2818 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 ... (remaining 21486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 28544 1.76 - 3.51: 509 3.51 - 5.27: 79 5.27 - 7.03: 36 7.03 - 8.79: 4 Bond angle restraints: 29172 Sorted by residual: angle pdb=" N ILE A2479 " pdb=" CA ILE A2479 " pdb=" C ILE A2479 " ideal model delta sigma weight residual 113.71 109.93 3.78 9.50e-01 1.11e+00 1.59e+01 angle pdb=" C GLU A2520 " pdb=" N ASN A2521 " pdb=" CA ASN A2521 " ideal model delta sigma weight residual 122.46 127.01 -4.55 1.41e+00 5.03e-01 1.04e+01 angle pdb=" CB GLU C 386 " pdb=" CG GLU C 386 " pdb=" CD GLU C 386 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.70e+00 3.46e-01 9.41e+00 angle pdb=" CG MET A2428 " pdb=" SD MET A2428 " pdb=" CE MET A2428 " ideal model delta sigma weight residual 100.90 94.69 6.21 2.20e+00 2.07e-01 7.96e+00 angle pdb=" CB GLN A1665 " pdb=" CG GLN A1665 " pdb=" CD GLN A1665 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.70e+00 3.46e-01 7.73e+00 ... (remaining 29167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.37: 12180 26.37 - 52.74: 597 52.74 - 79.11: 34 79.11 - 105.48: 9 105.48 - 131.84: 1 Dihedral angle restraints: 12821 sinusoidal: 4941 harmonic: 7880 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 -136.61 -131.84 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" CA GLU A2164 " pdb=" C GLU A2164 " pdb=" N ALA A2165 " pdb=" CA ALA A2165 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 169.87 -78.32 1 2.00e+01 2.50e-03 1.91e+01 ... (remaining 12818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2285 0.037 - 0.074: 753 0.074 - 0.110: 252 0.110 - 0.147: 69 0.147 - 0.184: 5 Chirality restraints: 3364 Sorted by residual: 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 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA GLU A2164 " pdb=" N GLU A2164 " pdb=" C GLU A2164 " pdb=" CB GLU A2164 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CB ILE C 281 " pdb=" CA ILE C 281 " pdb=" CG1 ILE C 281 " pdb=" CG2 ILE C 281 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 3361 not shown) Planarity restraints: 3669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2491 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A2492 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A2492 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2492 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A2619 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2920 " 0.015 2.00e-02 2.50e+03 1.20e-02 3.59e+00 pdb=" CG TRP A2920 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A2920 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A2920 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2920 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A2920 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2920 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2920 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2920 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A2920 " 0.006 2.00e-02 2.50e+03 ... (remaining 3666 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 207 2.60 - 3.18: 17282 3.18 - 3.75: 33271 3.75 - 4.33: 42953 4.33 - 4.90: 73142 Nonbonded interactions: 166855 Sorted by model distance: nonbonded pdb=" OD2 ASP A1848 " pdb="MG MG A4105 " model vdw 2.029 2.170 nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.042 2.170 nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.129 2.170 nonbonded pdb=" OG SER C 226 " pdb=" OD1 ASP C 228 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP A1823 " pdb=" N ASP A1824 " model vdw 2.276 3.120 ... (remaining 166850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.910 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: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.038 21491 Z= 0.135 Angle : 0.603 8.786 29172 Z= 0.305 Chirality : 0.043 0.184 3364 Planarity : 0.004 0.060 3669 Dihedral : 14.384 131.844 7697 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2660 helix: 1.33 (0.13), residues: 1383 sheet: -0.11 (0.32), residues: 313 loop : -0.96 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3510 TYR 0.023 0.001 TYR A3330 PHE 0.026 0.001 PHE A2972 TRP 0.032 0.001 TRP A2920 HIS 0.013 0.001 HIS A3413 Details of bonding type rmsd covalent geometry : bond 0.00301 (21491) covalent geometry : angle 0.60293 (29172) hydrogen bonds : bond 0.14474 ( 1192) hydrogen bonds : angle 6.08499 ( 3504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 2801 LYS cc_start: 0.8819 (tttm) cc_final: 0.8202 (ttmm) REVERT: A 2805 ASP cc_start: 0.7399 (m-30) cc_final: 0.7124 (m-30) REVERT: A 2829 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 2944 ILE cc_start: 0.8541 (mt) cc_final: 0.8307 (tt) REVERT: A 3345 MET cc_start: 0.8669 (tpp) cc_final: 0.8188 (mmm) REVERT: A 3520 THR cc_start: 0.8466 (m) cc_final: 0.8211 (m) REVERT: A 3698 MET cc_start: 0.8004 (ttp) cc_final: 0.7739 (ttp) REVERT: C 230 GLN cc_start: 0.8496 (mt0) cc_final: 0.7926 (mt0) REVERT: C 419 TRP cc_start: 0.8788 (m-10) cc_final: 0.7554 (m-10) REVERT: C 436 ASP cc_start: 0.8010 (p0) cc_final: 0.7749 (p0) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1367 time to fit residues: 66.3136 Evaluate side-chains 217 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2735 HIS A2789 HIS A2845 GLN A3472 HIS ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112803 restraints weight = 36259.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115192 restraints weight = 20114.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116461 restraints weight = 14181.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117128 restraints weight = 11111.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117214 restraints weight = 10503.503| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21491 Z= 0.152 Angle : 0.540 7.870 29172 Z= 0.277 Chirality : 0.041 0.191 3364 Planarity : 0.004 0.050 3669 Dihedral : 5.684 130.871 2930 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.58 % Allowed : 9.31 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.16), residues: 2660 helix: 2.10 (0.14), residues: 1384 sheet: -0.14 (0.30), residues: 332 loop : -0.83 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3510 TYR 0.018 0.001 TYR C 219 PHE 0.015 0.001 PHE A2972 TRP 0.018 0.001 TRP A3676 HIS 0.006 0.001 HIS A2459 Details of bonding type rmsd covalent geometry : bond 0.00350 (21491) covalent geometry : angle 0.53969 (29172) hydrogen bonds : bond 0.03734 ( 1192) hydrogen bonds : angle 4.34320 ( 3504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1661 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 2164 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: A 2275 ILE cc_start: 0.6918 (tp) cc_final: 0.6532 (mm) REVERT: A 2801 LYS cc_start: 0.8882 (tttm) cc_final: 0.8333 (ttmm) REVERT: A 2805 ASP cc_start: 0.7417 (m-30) cc_final: 0.7092 (m-30) REVERT: A 2875 ASP cc_start: 0.8002 (m-30) cc_final: 0.7698 (m-30) REVERT: A 2944 ILE cc_start: 0.8594 (mt) cc_final: 0.8359 (tt) REVERT: A 3330 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 3345 MET cc_start: 0.8705 (tpp) cc_final: 0.8240 (mmm) REVERT: A 3510 ARG cc_start: 0.8393 (tpt90) cc_final: 0.8115 (tpt90) REVERT: A 3520 THR cc_start: 0.8351 (m) cc_final: 0.8092 (m) REVERT: A 3698 MET cc_start: 0.7917 (ttp) cc_final: 0.7678 (ttp) REVERT: A 3707 LYS cc_start: 0.8046 (mmpt) cc_final: 0.5951 (mttm) REVERT: A 3767 PHE cc_start: 0.7792 (t80) cc_final: 0.7579 (t80) REVERT: A 3905 ASP cc_start: 0.7471 (t0) cc_final: 0.7256 (t0) REVERT: C 230 GLN cc_start: 0.8480 (mt0) cc_final: 0.8024 (mt0) REVERT: C 419 TRP cc_start: 0.8882 (m-10) cc_final: 0.7667 (m-10) outliers start: 13 outliers final: 8 residues processed: 260 average time/residue: 0.1446 time to fit residues: 61.1465 Evaluate side-chains 231 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3409 ASP Chi-restraints excluded: chain A residue 3758 SER Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 279 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 192 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** A1864 ASN ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115173 restraints weight = 36102.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116953 restraints weight = 20445.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118390 restraints weight = 13848.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119224 restraints weight = 11744.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119155 restraints weight = 10576.601| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21491 Z= 0.102 Angle : 0.493 7.237 29172 Z= 0.249 Chirality : 0.040 0.154 3364 Planarity : 0.003 0.042 3669 Dihedral : 5.505 128.548 2930 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.08 % Allowed : 11.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.17), residues: 2660 helix: 2.40 (0.14), residues: 1385 sheet: -0.19 (0.29), residues: 339 loop : -0.78 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 356 TYR 0.019 0.001 TYR A2571 PHE 0.016 0.001 PHE A2972 TRP 0.019 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00223 (21491) covalent geometry : angle 0.49286 (29172) hydrogen bonds : bond 0.03251 ( 1192) hydrogen bonds : angle 4.02553 ( 3504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1650 LEU cc_start: 0.8690 (tp) cc_final: 0.8294 (mt) REVERT: A 1827 ASP cc_start: 0.8033 (p0) cc_final: 0.7818 (p0) REVERT: A 1986 GLU cc_start: 0.8148 (pm20) cc_final: 0.7487 (pm20) REVERT: A 2164 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 2275 ILE cc_start: 0.6915 (tp) cc_final: 0.6562 (mm) REVERT: A 2801 LYS cc_start: 0.8864 (tttm) cc_final: 0.8332 (ttmm) REVERT: A 2805 ASP cc_start: 0.7467 (m-30) cc_final: 0.7224 (m-30) REVERT: A 2829 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 2875 ASP cc_start: 0.8016 (m-30) cc_final: 0.7676 (m-30) REVERT: A 2880 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7911 (tp30) REVERT: A 2944 ILE cc_start: 0.8561 (mt) cc_final: 0.8342 (tt) REVERT: A 3330 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7961 (t80) REVERT: A 3345 MET cc_start: 0.8742 (tpp) cc_final: 0.8265 (mmm) REVERT: A 3510 ARG cc_start: 0.8286 (tpt90) cc_final: 0.8085 (tpt90) REVERT: A 3698 MET cc_start: 0.7964 (ttp) cc_final: 0.7706 (ttp) REVERT: A 3707 LYS cc_start: 0.7946 (mmpt) cc_final: 0.5894 (mttm) REVERT: C 230 GLN cc_start: 0.8498 (mt0) cc_final: 0.8036 (mt0) REVERT: C 337 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: C 419 TRP cc_start: 0.8839 (m-10) cc_final: 0.7638 (m-10) outliers start: 24 outliers final: 13 residues processed: 259 average time/residue: 0.1409 time to fit residues: 60.2906 Evaluate side-chains 241 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2508 GLN Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3633 GLU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 463 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 62 optimal weight: 0.5980 chunk 92 optimal weight: 0.0170 chunk 213 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 227 optimal weight: 0.0070 chunk 170 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2444 ASN A2787 HIS ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114862 restraints weight = 36130.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117488 restraints weight = 20056.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118826 restraints weight = 13647.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119585 restraints weight = 10869.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119666 restraints weight = 10161.254| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21491 Z= 0.100 Angle : 0.483 8.525 29172 Z= 0.244 Chirality : 0.040 0.153 3364 Planarity : 0.003 0.039 3669 Dihedral : 5.420 127.483 2930 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.39 % Allowed : 12.72 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.17), residues: 2660 helix: 2.59 (0.14), residues: 1375 sheet: -0.15 (0.30), residues: 339 loop : -0.71 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 356 TYR 0.016 0.001 TYR A2571 PHE 0.026 0.001 PHE A1734 TRP 0.018 0.001 TRP A3676 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00221 (21491) covalent geometry : angle 0.48302 (29172) hydrogen bonds : bond 0.03078 ( 1192) hydrogen bonds : angle 3.86519 ( 3504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9180 (mmt) cc_final: 0.8709 (mmt) REVERT: A 1650 LEU cc_start: 0.8724 (tp) cc_final: 0.8221 (mt) REVERT: A 1827 ASP cc_start: 0.7883 (p0) cc_final: 0.7603 (p0) REVERT: A 2164 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 2275 ILE cc_start: 0.6890 (tp) cc_final: 0.6576 (mm) REVERT: A 2801 LYS cc_start: 0.8903 (tttm) cc_final: 0.8374 (ttmm) REVERT: A 2805 ASP cc_start: 0.7460 (m-30) cc_final: 0.7222 (m-30) REVERT: A 2875 ASP cc_start: 0.7999 (m-30) cc_final: 0.7621 (m-30) REVERT: A 2880 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 2980 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7236 (mmp) REVERT: A 3330 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.8031 (t80) REVERT: A 3345 MET cc_start: 0.8715 (tpp) cc_final: 0.8195 (mmm) REVERT: A 3510 ARG cc_start: 0.8311 (tpt90) cc_final: 0.8026 (tpt-90) REVERT: A 3623 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7903 (ptpp) REVERT: A 3698 MET cc_start: 0.7965 (ttp) cc_final: 0.7613 (ttp) REVERT: A 3707 LYS cc_start: 0.7924 (mmpt) cc_final: 0.5866 (mttm) REVERT: C 230 GLN cc_start: 0.8522 (mt0) cc_final: 0.8090 (mt0) REVERT: C 260 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7770 (mmmt) REVERT: C 337 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: C 386 GLU cc_start: 0.6948 (tp30) cc_final: 0.6414 (tm-30) REVERT: C 419 TRP cc_start: 0.8820 (m-10) cc_final: 0.7604 (m-10) outliers start: 31 outliers final: 20 residues processed: 263 average time/residue: 0.1318 time to fit residues: 57.7777 Evaluate side-chains 240 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2508 GLN Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 463 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 15 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 246 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 253 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 0.0050 overall best weight: 0.2510 ------------------------------------------------------------------------------- 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** A1967 HIS ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117439 restraints weight = 36079.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118983 restraints weight = 20453.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120430 restraints weight = 14721.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121039 restraints weight = 11943.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121061 restraints weight = 10736.455| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21491 Z= 0.088 Angle : 0.473 7.288 29172 Z= 0.238 Chirality : 0.039 0.161 3364 Planarity : 0.003 0.039 3669 Dihedral : 5.317 125.107 2930 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.39 % Allowed : 13.53 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.17), residues: 2660 helix: 2.64 (0.14), residues: 1380 sheet: -0.14 (0.29), residues: 339 loop : -0.64 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.016 0.001 TYR A2571 PHE 0.021 0.001 PHE A1734 TRP 0.018 0.001 TRP A2084 HIS 0.009 0.001 HIS A3624 Details of bonding type rmsd covalent geometry : bond 0.00184 (21491) covalent geometry : angle 0.47275 (29172) hydrogen bonds : bond 0.02913 ( 1192) hydrogen bonds : angle 3.74600 ( 3504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9166 (mmt) cc_final: 0.8683 (mmt) REVERT: A 1650 LEU cc_start: 0.8659 (tp) cc_final: 0.8220 (mt) REVERT: A 1827 ASP cc_start: 0.7827 (p0) cc_final: 0.7552 (p0) REVERT: A 2124 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: A 2275 ILE cc_start: 0.6874 (tp) cc_final: 0.6640 (mm) REVERT: A 2473 LEU cc_start: 0.8835 (tp) cc_final: 0.8465 (tt) REVERT: A 2801 LYS cc_start: 0.8854 (tttm) cc_final: 0.8325 (ttmm) REVERT: A 2805 ASP cc_start: 0.7485 (m-30) cc_final: 0.7216 (m-30) REVERT: A 2875 ASP cc_start: 0.7989 (m-30) cc_final: 0.7706 (m-30) REVERT: A 2880 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7998 (tp30) REVERT: A 2940 PHE cc_start: 0.7668 (m-10) cc_final: 0.7468 (p90) REVERT: A 3330 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 3345 MET cc_start: 0.8736 (tpp) cc_final: 0.8247 (mmm) REVERT: A 3414 MET cc_start: 0.8586 (mmt) cc_final: 0.8312 (mmm) REVERT: A 3510 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7994 (tpt-90) REVERT: A 3623 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7947 (ptpp) REVERT: A 3698 MET cc_start: 0.8017 (ttp) cc_final: 0.7669 (ttp) REVERT: A 3707 LYS cc_start: 0.7873 (mmpt) cc_final: 0.5921 (mttm) REVERT: A 3767 PHE cc_start: 0.7749 (t80) cc_final: 0.7489 (t80) REVERT: A 3788 MET cc_start: 0.9014 (ttp) cc_final: 0.8683 (ttt) REVERT: C 260 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7838 (mmmt) REVERT: C 337 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: C 370 MET cc_start: 0.6635 (pmm) cc_final: 0.6139 (pmm) REVERT: C 386 GLU cc_start: 0.6975 (tp30) cc_final: 0.6500 (tm-30) REVERT: C 419 TRP cc_start: 0.8760 (m-10) cc_final: 0.7515 (m-10) REVERT: C 428 GLN cc_start: 0.8322 (pm20) cc_final: 0.8025 (pm20) outliers start: 31 outliers final: 20 residues processed: 268 average time/residue: 0.1310 time to fit residues: 57.6155 Evaluate side-chains 247 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2508 GLN Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 248 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.140806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113396 restraints weight = 36066.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116777 restraints weight = 20183.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117256 restraints weight = 14267.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118681 restraints weight = 11163.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118688 restraints weight = 9547.870| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21491 Z= 0.118 Angle : 0.497 7.623 29172 Z= 0.248 Chirality : 0.040 0.165 3364 Planarity : 0.003 0.038 3669 Dihedral : 5.344 124.272 2930 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 14.25 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2660 helix: 2.67 (0.14), residues: 1382 sheet: -0.29 (0.29), residues: 347 loop : -0.64 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3514 TYR 0.012 0.001 TYR A2571 PHE 0.020 0.001 PHE A1734 TRP 0.014 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00273 (21491) covalent geometry : angle 0.49735 (29172) hydrogen bonds : bond 0.03083 ( 1192) hydrogen bonds : angle 3.72041 ( 3504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9184 (mmt) cc_final: 0.8867 (mmt) REVERT: A 1650 LEU cc_start: 0.8726 (tp) cc_final: 0.8198 (mt) REVERT: A 1827 ASP cc_start: 0.7901 (p0) cc_final: 0.7620 (p0) REVERT: A 2124 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: A 2164 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 2275 ILE cc_start: 0.6978 (tp) cc_final: 0.6656 (mm) REVERT: A 2801 LYS cc_start: 0.8867 (tttm) cc_final: 0.8341 (ttmm) REVERT: A 2805 ASP cc_start: 0.7390 (m-30) cc_final: 0.7155 (m-30) REVERT: A 2875 ASP cc_start: 0.8076 (m-30) cc_final: 0.7654 (m-30) REVERT: A 2880 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7968 (tp30) REVERT: A 3345 MET cc_start: 0.8730 (tpp) cc_final: 0.8212 (mmm) REVERT: A 3414 MET cc_start: 0.8621 (mmt) cc_final: 0.8337 (mmm) REVERT: A 3510 ARG cc_start: 0.8277 (tpt90) cc_final: 0.8027 (tpt90) REVERT: A 3623 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7934 (ptpp) REVERT: A 3698 MET cc_start: 0.8046 (ttp) cc_final: 0.7811 (ttp) REVERT: A 3707 LYS cc_start: 0.7975 (mmpt) cc_final: 0.6009 (mttt) REVERT: A 3767 PHE cc_start: 0.7760 (t80) cc_final: 0.7542 (t80) REVERT: C 260 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7801 (mmmt) REVERT: C 277 GLN cc_start: 0.8086 (mp10) cc_final: 0.7867 (mp10) REVERT: C 337 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: C 428 GLN cc_start: 0.8341 (pm20) cc_final: 0.8059 (pm20) outliers start: 37 outliers final: 23 residues processed: 254 average time/residue: 0.1288 time to fit residues: 53.9776 Evaluate side-chains 244 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2063 MET Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 84 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 67 optimal weight: 0.1980 chunk 116 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1967 HIS ** A2167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2854 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115983 restraints weight = 36053.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117597 restraints weight = 20207.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118686 restraints weight = 14453.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119454 restraints weight = 12029.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119475 restraints weight = 10893.854| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21491 Z= 0.098 Angle : 0.490 8.413 29172 Z= 0.243 Chirality : 0.040 0.166 3364 Planarity : 0.003 0.038 3669 Dihedral : 5.291 122.959 2930 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 15.02 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.17), residues: 2660 helix: 2.71 (0.14), residues: 1383 sheet: -0.23 (0.29), residues: 344 loop : -0.59 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3514 TYR 0.013 0.001 TYR A2571 PHE 0.016 0.001 PHE A1734 TRP 0.018 0.001 TRP C 299 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00219 (21491) covalent geometry : angle 0.49005 (29172) hydrogen bonds : bond 0.02939 ( 1192) hydrogen bonds : angle 3.66567 ( 3504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9226 (mmt) cc_final: 0.8946 (mmt) REVERT: A 1650 LEU cc_start: 0.8680 (tp) cc_final: 0.8192 (mt) REVERT: A 1827 ASP cc_start: 0.7881 (p0) cc_final: 0.7556 (p0) REVERT: A 1921 MET cc_start: 0.7744 (mtt) cc_final: 0.7457 (mtt) REVERT: A 2124 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: A 2164 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 2275 ILE cc_start: 0.6943 (tp) cc_final: 0.6656 (mm) REVERT: A 2801 LYS cc_start: 0.8869 (tttm) cc_final: 0.8346 (ttmm) REVERT: A 2805 ASP cc_start: 0.7453 (m-30) cc_final: 0.7202 (m-30) REVERT: A 2880 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7987 (tp30) REVERT: A 2940 PHE cc_start: 0.7719 (m-10) cc_final: 0.7470 (p90) REVERT: A 3345 MET cc_start: 0.8723 (tpp) cc_final: 0.8200 (mmm) REVERT: A 3414 MET cc_start: 0.8583 (mmt) cc_final: 0.8329 (mmm) REVERT: A 3510 ARG cc_start: 0.8284 (tpt90) cc_final: 0.8034 (tpt90) REVERT: A 3623 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7899 (ptpp) REVERT: A 3698 MET cc_start: 0.8040 (ttp) cc_final: 0.7691 (ttp) REVERT: A 3707 LYS cc_start: 0.7909 (mmpt) cc_final: 0.5994 (mttt) REVERT: A 3767 PHE cc_start: 0.7771 (t80) cc_final: 0.7557 (t80) REVERT: C 260 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7685 (mmmt) REVERT: C 337 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: C 370 MET cc_start: 0.6765 (pmm) cc_final: 0.6244 (pmm) REVERT: C 428 GLN cc_start: 0.8415 (pm20) cc_final: 0.8086 (pm20) outliers start: 37 outliers final: 25 residues processed: 251 average time/residue: 0.1216 time to fit residues: 50.5847 Evaluate side-chains 241 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2048 SER Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3633 GLU Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 12 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 chunk 255 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112413 restraints weight = 35914.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115461 restraints weight = 20050.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117460 restraints weight = 13726.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118546 restraints weight = 10726.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119515 restraints weight = 9230.209| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21491 Z= 0.120 Angle : 0.512 9.711 29172 Z= 0.254 Chirality : 0.041 0.357 3364 Planarity : 0.003 0.038 3669 Dihedral : 5.336 123.285 2930 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.66 % Allowed : 15.02 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2660 helix: 2.70 (0.14), residues: 1384 sheet: -0.24 (0.29), residues: 345 loop : -0.60 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3514 TYR 0.013 0.001 TYR A2571 PHE 0.016 0.001 PHE A1734 TRP 0.015 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00278 (21491) covalent geometry : angle 0.51168 (29172) hydrogen bonds : bond 0.03055 ( 1192) hydrogen bonds : angle 3.66979 ( 3504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9224 (mmt) cc_final: 0.8944 (mmt) REVERT: A 1650 LEU cc_start: 0.8743 (tp) cc_final: 0.8173 (mt) REVERT: A 1827 ASP cc_start: 0.7933 (p0) cc_final: 0.7605 (p0) REVERT: A 1921 MET cc_start: 0.7695 (mtt) cc_final: 0.7411 (mtt) REVERT: A 2124 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: A 2164 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 2275 ILE cc_start: 0.6979 (tp) cc_final: 0.6706 (mm) REVERT: A 2801 LYS cc_start: 0.8811 (tttm) cc_final: 0.8292 (ttmm) REVERT: A 2805 ASP cc_start: 0.7207 (m-30) cc_final: 0.7003 (m-30) REVERT: A 2875 ASP cc_start: 0.8073 (m-30) cc_final: 0.7742 (m-30) REVERT: A 2880 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 3345 MET cc_start: 0.8743 (tpp) cc_final: 0.8286 (tpp) REVERT: A 3414 MET cc_start: 0.8580 (mmt) cc_final: 0.8364 (mmm) REVERT: A 3510 ARG cc_start: 0.8271 (tpt90) cc_final: 0.8039 (tpt90) REVERT: A 3623 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (ptpp) REVERT: A 3698 MET cc_start: 0.8015 (ttp) cc_final: 0.7694 (ttp) REVERT: A 3707 LYS cc_start: 0.8074 (mmpt) cc_final: 0.6011 (mttm) REVERT: A 3767 PHE cc_start: 0.7773 (t80) cc_final: 0.7563 (t80) REVERT: C 260 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7692 (mmmt) REVERT: C 370 MET cc_start: 0.6866 (pmm) cc_final: 0.6287 (pmm) REVERT: C 428 GLN cc_start: 0.8386 (pm20) cc_final: 0.8042 (pm20) REVERT: C 442 TRP cc_start: 0.8433 (m100) cc_final: 0.8122 (m100) outliers start: 37 outliers final: 27 residues processed: 248 average time/residue: 0.1220 time to fit residues: 50.8537 Evaluate side-chains 249 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2048 SER Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 225 optimal weight: 0.8980 chunk 240 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1967 HIS A4022 GLN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112440 restraints weight = 35959.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115534 restraints weight = 20078.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117534 restraints weight = 13667.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118853 restraints weight = 10659.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119585 restraints weight = 9076.000| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21491 Z= 0.103 Angle : 0.507 11.620 29172 Z= 0.251 Chirality : 0.040 0.405 3364 Planarity : 0.003 0.038 3669 Dihedral : 5.293 122.402 2930 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.57 % Allowed : 15.51 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.17), residues: 2660 helix: 2.71 (0.14), residues: 1386 sheet: -0.20 (0.29), residues: 344 loop : -0.58 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3514 TYR 0.018 0.001 TYR A2571 PHE 0.015 0.001 PHE A2972 TRP 0.018 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00233 (21491) covalent geometry : angle 0.50722 (29172) hydrogen bonds : bond 0.02941 ( 1192) hydrogen bonds : angle 3.63449 ( 3504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9226 (mmt) cc_final: 0.8957 (mmt) REVERT: A 1650 LEU cc_start: 0.8720 (tp) cc_final: 0.8165 (mt) REVERT: A 1827 ASP cc_start: 0.7856 (p0) cc_final: 0.7522 (p0) REVERT: A 2124 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: A 2164 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 2801 LYS cc_start: 0.8804 (tttm) cc_final: 0.8296 (ttmm) REVERT: A 2805 ASP cc_start: 0.7278 (m-30) cc_final: 0.7047 (m-30) REVERT: A 2875 ASP cc_start: 0.8075 (m-30) cc_final: 0.7739 (m-30) REVERT: A 2880 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7922 (tp30) REVERT: A 2938 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7684 (ppp) REVERT: A 3345 MET cc_start: 0.8719 (tpp) cc_final: 0.8251 (tpp) REVERT: A 3414 MET cc_start: 0.8569 (mmt) cc_final: 0.8353 (mmm) REVERT: A 3510 ARG cc_start: 0.8259 (tpt90) cc_final: 0.8032 (tpt90) REVERT: A 3623 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7863 (ptpp) REVERT: A 3698 MET cc_start: 0.8008 (ttp) cc_final: 0.7744 (ttp) REVERT: A 3707 LYS cc_start: 0.8006 (mmpt) cc_final: 0.5911 (mttm) REVERT: A 3767 PHE cc_start: 0.7770 (t80) cc_final: 0.7568 (t80) REVERT: C 260 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7722 (mmmt) REVERT: C 370 MET cc_start: 0.6920 (pmm) cc_final: 0.6293 (pmm) REVERT: C 428 GLN cc_start: 0.8393 (pm20) cc_final: 0.8059 (pm20) REVERT: C 442 TRP cc_start: 0.8389 (m100) cc_final: 0.8095 (m100) outliers start: 35 outliers final: 27 residues processed: 242 average time/residue: 0.1314 time to fit residues: 53.2357 Evaluate side-chains 242 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2048 SER Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2938 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3890 GLN Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 210 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 174 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113542 restraints weight = 36044.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116625 restraints weight = 20008.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118640 restraints weight = 13644.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119894 restraints weight = 10610.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120542 restraints weight = 9024.429| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21491 Z= 0.121 Angle : 0.523 11.422 29172 Z= 0.258 Chirality : 0.041 0.407 3364 Planarity : 0.003 0.037 3669 Dihedral : 5.349 122.760 2930 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.66 % Allowed : 15.38 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.17), residues: 2660 helix: 2.68 (0.14), residues: 1391 sheet: -0.21 (0.29), residues: 349 loop : -0.58 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3514 TYR 0.018 0.001 TYR A3364 PHE 0.016 0.001 PHE A2972 TRP 0.015 0.001 TRP A2084 HIS 0.010 0.001 HIS A3413 Details of bonding type rmsd covalent geometry : bond 0.00284 (21491) covalent geometry : angle 0.52337 (29172) hydrogen bonds : bond 0.03073 ( 1192) hydrogen bonds : angle 3.65663 ( 3504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 1562 MET cc_start: 0.9220 (mmt) cc_final: 0.8954 (mmt) REVERT: A 1650 LEU cc_start: 0.8745 (tp) cc_final: 0.8164 (mt) REVERT: A 1827 ASP cc_start: 0.7913 (p0) cc_final: 0.7594 (p0) REVERT: A 1921 MET cc_start: 0.7672 (mtt) cc_final: 0.7436 (mtt) REVERT: A 2124 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: A 2164 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 2801 LYS cc_start: 0.8812 (tttm) cc_final: 0.8295 (ttmm) REVERT: A 2805 ASP cc_start: 0.7281 (m-30) cc_final: 0.7055 (m-30) REVERT: A 2875 ASP cc_start: 0.8094 (m-30) cc_final: 0.7812 (m-30) REVERT: A 2880 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7925 (tp30) REVERT: A 2938 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7645 (ppp) REVERT: A 3345 MET cc_start: 0.8715 (tpp) cc_final: 0.8241 (tpp) REVERT: A 3510 ARG cc_start: 0.8274 (tpt90) cc_final: 0.8056 (tpt90) REVERT: A 3623 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7907 (ptpp) REVERT: A 3707 LYS cc_start: 0.8138 (mmpt) cc_final: 0.5975 (mttm) REVERT: C 260 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7729 (mmmt) REVERT: C 322 THR cc_start: 0.7326 (p) cc_final: 0.7075 (p) REVERT: C 370 MET cc_start: 0.7046 (pmm) cc_final: 0.6440 (pmm) REVERT: C 428 GLN cc_start: 0.8406 (pm20) cc_final: 0.8069 (pm20) REVERT: C 442 TRP cc_start: 0.8420 (m100) cc_final: 0.8112 (m100) outliers start: 37 outliers final: 26 residues processed: 249 average time/residue: 0.1294 time to fit residues: 53.1682 Evaluate side-chains 245 residues out of total 2459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2048 SER Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2124 GLU Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2170 LEU Chi-restraints excluded: chain A residue 2210 CYS Chi-restraints excluded: chain A residue 2407 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2840 ILE Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2922 THR Chi-restraints excluded: chain A residue 2938 MET Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3477 VAL Chi-restraints excluded: chain A residue 3623 LYS Chi-restraints excluded: chain A residue 3626 VAL Chi-restraints excluded: chain A residue 3679 TYR Chi-restraints excluded: chain A residue 3972 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 12 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1967 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115141 restraints weight = 36006.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118277 restraints weight = 19781.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120300 restraints weight = 13332.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121631 restraints weight = 10317.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122438 restraints weight = 8737.435| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21491 Z= 0.101 Angle : 0.513 11.903 29172 Z= 0.253 Chirality : 0.041 0.399 3364 Planarity : 0.003 0.037 3669 Dihedral : 5.288 121.349 2930 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.53 % Allowed : 15.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.17), residues: 2660 helix: 2.71 (0.14), residues: 1392 sheet: -0.19 (0.29), residues: 343 loop : -0.55 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3670 TYR 0.030 0.001 TYR A3364 PHE 0.018 0.001 PHE A3767 TRP 0.018 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00227 (21491) covalent geometry : angle 0.51298 (29172) hydrogen bonds : bond 0.02911 ( 1192) hydrogen bonds : angle 3.62114 ( 3504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.42 seconds wall clock time: 55 minutes 52.69 seconds (3352.69 seconds total)